For a complete list click here [pubmed link]

 

Microbiome and Metabolites

A widely distributed gene cluster compensates for uricase loss in hominids.

Liu, Y., Jarman, J.B., Low, Y.S., Augutijn, H.E., Huang, S., Chen, H., DeFeo, M.E., Sekiba, K., Hou, B., Meng, X., Weakley, A.M. Cabrera, A.V., Zhou, Z., van Wezel, G., Medema, M.H., Ganesan, C., Pao, A.C., Gombar, S., and Dodd, D.

Cell 2023 186(16):3400-3413.e20. [article link]

Targeted Quantification of Amino Acids by Dansylation.

Liu, Y., Chen, H., and Dodd, D.

Methods in Molecular Biology 2023 2675:65-76. [article link]

Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta.

Noecker, C., Sanchez, J., Bisanz, J.E., Escalante, V., Alexander, M., Trepka, K., Heinken, A., Liu, Y., Dodd, D., Thiele, I., DeFelice, B.C., and Turnbaugh, P.J.

PLoS Biology 2023 21(5):e3002125. [article link]

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.

Andreu, V.P., Augustijn, H.E., Chen, L., Zhernakova, A., Fun, J., Fischbach, M.A., Dodd, D., and Medema, M.H.

Nature Biotechnology 2023 10.1038/s41587-023-01675-1. [article link]

Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid.

Pruss, K.M., Chen, H., Liu, Y., Van Treuren, W., Higginbottom, S.K., Jarman, J.B., Fischer, C.R., Mak, J., Wong, B., Cowan, T.M., Fischbach, M.A., Sonnenburg, J.L., and Dodd, D.

Nature Communications 2023 14, 512. [article link]

Tutorial: Microbiome studies in drug metabolism.

Dodd, D., and Cann, I.

Clinical and Translational Science 2022 15(12):2812-2837. [article link]

Role of insulin resistance and the gut microbiome on urine oxalate excretion in ob/ob mice.

Xiang, H., Chen, H., Liu, Y., Dodd, D., and Pao, AC.

Physiological Reports 2022 10:(14):e15357. [article link]

The gut metabolite indole-3 propionate promotes nerve regeneration and repair.

Serger, E., Luego-Gutierrez, L., Chadwick, J.S., Kong, G., Zhou, L., Crawford, G., Danzi, M.C., Myridakis, A., Brandis, A., Bello, A.T., Müller F., Sanchez-Vassopoulos, A., De Virgiliis, F., Liddell, P., Dumas, M.E., Strid, J., Mani, S., Dodd, D., and Di Giovanni, S.

Nature 2022 607(7919):585-592. [article link]

Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites.

Liu, Y., Chen, H., Van Treuren, W., Hou, B.H., Higginbottom, S.K., and Dodd, D.

Nature Microbiology 2022 7(5):695-706. [article link]

A metabolomics pipeline for the mechanistic interrogation of the gut microbiome.

Han, S., Van Treuren, W., Fischer, C.R., Merrill, B.D., DeFelice, B.C., Sanchez, J.M., Higginbottom, S.K., Guthrie, L., Fall, L.A., Dodd, D., Fischbach, M.A., and Sonnenburg, J.L.

Nature 2021 595(7867):415-420. [article link]

The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota.

Pascal Andreu, V., Roel-Touris, J., Dodd, D., Fischbach, M.A., and Medema, M.H.

Nucleic Acids Research 2021 49(W1):W263-W270. [article link]

Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade.

Sun, S., Luo, L., Liang, W., Yin, Q., Guo, J., Rush, A.M., Lv, Z., Liang, Q., Fischbach, M.A., Sonnenburg, J.L., Dodd, D., Davis, M.M., and Wang, F.

Proceedings of the National Academy of Sciences 2020 117(44):27509-27515. [article link]

Microbial contribution to the human metabolome: Implications for health and disease.

Van Treuren, W. and D. Dodd.

Annual Review of Pathology 2020 15:345-369. [article link]

Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.

Pareek, S., Kurakawa, T., Das, B., Motooka, D., Nakaya, S., Rongsen-Chandola, T., Goyal, N., Kayama, H., Dodd, D., Okumura, R., Maeda, Y., Fujimoto, K., Nii, T., Ogawa, T., Iida, T., Bhandari, N., Kida, T., Nakamura, S., Nair, G. B., and Takeda, K.

NPJ Biofilms and Microbiomes 2019 5:37. [article link]

Depletion of microbiome-derived molecules in the host using Clostridium genetics.

Guo, C. J., Allen, B. M., Hiam, K. J., Dodd, D., Van Treuren, W., Higginbottom, S., Nagashima, K., Fischer, C. R., Sonnenburg, J. L., Spitzer, M. H., and Fischbach, M. A.

Science 2019 366 (6471) [article link]

Perspective: Dietary biomarkers of intake and exposure—Exploration with omics approaches.

Maruvada, P., Lampe, J. W., Wishart, D. S., Barupal, D., Chester, D. N., Dodd, D., Djoumbou-Feunang, Y., Dorrestein, P. C., Dragsted, L. O., Draper, J., Duffy, L. C., Dwyer, J. T., Emenaker, N. J., Fiehn, O., Gerszten, R. E., B Hu, F., Karp, R. W., Klurfeld, D. M., Laughlin, M. R., Little, A. R., Lynch, C. J., Moore, S. C., Nicastro, H. L., O'Brien, D. M., Ordovás, J. M., Osganian, S. K., Playdon, M., Prentice, R., Raftery, D., Reisdorph, N., Roche, H. M., Ross, S. A., Sang, S., Scalbert, A., Srinivas, P. R., and Zeisel, S. H.

Advances in Nutrition 2019 Aug 6. [article link]

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. L.

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.

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 urinary free cortisol assay by tandem mass spectrometry.

Luo A, El Gierari ETM, Nally LM, Sturmer LR, Dodd D, Shi RZ.

Steroids 2019 146: 65-69. [article link]

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

Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization.

Pruss, K.M., Enam, F., Battaglioli, E., DeFeo, M., Diaz, O.R., Higginbottom, S.K., Fischer, C.R., Hryckowian, A.J., Van Treuren, W., Dodd, D., Kashyap, P., and Sonnenburg, J.L.

Nature Metabolism 2022 4(1):19-28. [article link]

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]