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Emmanuel F. Mongodin

Emmanuel F. Mongodin Ph.D.

Academic Title: Assistant Professor
Primary Appointment: Microbiology and Immunology
Additional Title(s): Assistant Professor, Institute for Genome Sciences
Location: HSF-II S-403C
Phone: (410) 706-6717
Fax: (410) 706-6756

Personal History:

Originally trained as a physiologist, Emmanuel Mongodin is a leading genomics and microbiology scientist at the Institute for Genome Sciences (IGS) and an Assistant Professor in Microbiology and Immunology at the University of Maryland School of Medicine in Baltimore, Maryland. His primary research interests focus on the application of microbial genomics, comparative genomics and metagenomic approaches to the study of host-bacteria interactions and the microbial populations colonizing the human body.

  • B.Sc., 1995, Cellular Biology and Physiology, option Cellular and Molecular Genetic. Université d'Angers, France.
  • M.Sc., 1996, Physiology and Pathology of the Respiratory and Circulatory Systems. Université Paris VII – Denis Diderot, France.
  • Ph.D., 1997-2000, Biological and Medical Engineering. Université de Reims-Champagne-Ardenne, France.
  • Post-doctoral fellow, 2001-2002, Virginia Commonwealth University (Richmond, VA), Division of Infectious Diseases (Dr. Gordon L. Archer).
  • Staff Scientist I, 2002-2004, The Institute for Genomic Research (TIGR), Microbial Genomics Department (Dr. Karen E. Nelson).
  • Staff Scientist II, 2005-2007, The J. Craig Venter Institute (formerly The Institute for Genomic Research - TIGR), Infectious Diseases Department (Dr. Karen E. Nelson).
  • Assistant Professor, 2007-present, Institute for Genome Sciences and University of Maryland School of Medicine

Research Interests:

My research focuses on the application of microbial genomics to two main topics. The first one concerns the sequencing and comparative genomics analysis of seventeen (17) strains of Borrelia sp. (, the causative agent of Lyme disease. Secondly, my research also focuses on human metagenomics, also called community genomics and defined as "the application of modern genomics techniques to the study of complex communities of microbial organisms (e.g. the microbiome) directly in their natural environments (e.g. the human body)". This new field of research is still in its infancy, but because of its potential to sample the body’s microbiome both widely and deeply, the field holds great promises for the development of new strategies for diagnosing, treating and possibly preventing a wide range of human diseases.


Peer-Reviewed Articles

DeBoy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson NE. Insights into Plant Cell-wall Degradation from the Genome Sequence of the Soil Bacterium Cellvibrio japonicus. Submitted to Journal of Bacteriology.

Ashby MN, Rine J, Mongodin EF, Nelson KE, Dimster-Denk D. Serial Analysis of Ribosomal DNA and the Unexpected Dominance of Rare Members of Microbial Communities. Applied and Environmental Microbiology, 2007 Jul;73(14):4532-42.

Shapir N, Mongodin EF, Sadowsky MJ, Daugherty SC, Nelson KE, Wackett LP. Evolution of Catabolic Pathways: Genomic Insights into Microbial s-Triazine Metabolism. Journal of Bacteriology, 2007, Feb;189(3):674-82.

Mongodin EF, Shapir N, Daugherty SC, Deboy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. Secrets of Soil Survival Revealed by the Genome Sequence of Arthrobacter aurescens TC1. PLoS Genetics, 2006 Dec 22;2(12):e214

Centeno MS, Guerreiro CI, Dias FM, Morland C, Tailford LE, Goyal A, Prates JA, Ferreira LM, Caldeira RM, Mongodin EF, Nelson KE, Gilbert HJ, Fontes CM. Galactomannan hydrolysis and mannose metabolism in Cellvibrio mixtus. FEMS Microbiology Letters. 2006, Aug;261(1):123-32.

Pieper R, Gatlin T, Parmar P, Huang ST, Clark D, Mongodin EF, Gill SR, Peterson S. Clear protein expression changes comparing three Staphylococcus aureus isolates with different susceptibilities to vancomycin revealed by classical proteomic profiling. Proteomics. 2006, Aug;6(15):4246-58.

DeBoy RT, Mongodin EF, Emerson JB Nelson KE. Genome shuffling in the Thermotogales: involvement of CRISPRs and tRNA genes.  Journal of Bacteriology, 2006, Apr;188(7):2364-74.

Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F, Lin J, Carleton HA, Mongodin EF, Sensabaugh GF, Perdreau-Remington F. Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus. The Lancet, 2006, Mar 4;367(9512):731-9.

Gatlin CL, Pieper R, Huang ST, Mongodin EF, Gebregeorgis E, Parmar PP, Clark DJ, Alami H, Papazisi L, Fleischmann RD, Gill SR, Peterson SN. Proteomic Profiling of Cell Envelope-Associated Proteins from Staphylococcus aureus. Proteomics, 2006 Mar;6(5):1530-49.

Mongodin EF, Nelson KE, Daugherty S, Deboy RT, Wister J, Khouri H, Weidman J, Walsh DA, Papke RT, Sanchez Perez G, Sharma AK, Nesbo CL, MacLeod D, Bapteste E, Doolittle WF, Charlebois RL, Legault B, Rodriguez-Valera F. The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.  Proc Natl Acad Sci U S A. 2005, 102(50):18147-52.

Haft DA, Selengut J, Mongodin EF and Nelson KE. A guild of forty-five CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Computational Biology, 2005, 1(6):e60.

Mongodin EF, Gill SR, Hance IR, DeBoy RT, Huber R, Stetter K, Nelson KE. Gene transfer in Thermotoga maritima, a model hyperthermophilic species. Journal of Bacteriology, 2005, 187(14):4935-4944.

Gill SR, Fouts DE, Archer G, Mongodin EF, DeBoy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty S, Nelson WC et al.  Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin resistant Staphylococcus aureus and a biofilm producing methicillin resistant Staphylococcus epidermidis. Journal of Bacteriology, 2005, 187(7):2426-2438.

Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, DeBoy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin S, Madupu R, Sullivan S, Shetty J, Ayodeji MA, Shvartsbeyn A, Fraser CM and Nelson KE.  Major structural differences and novel potential virulence mechanisms from the genomes of multiple Campylobacter species.. PLoS Biology, Jan 4th, 2005, e15.

Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli S, Gill SR et al.  Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species. Nucleic Acids Research 2004, 32: 2386-2395.

Mongodin E, Finan J, Climo MW, Gill S, Archer GL. Microarray transcription analysis of clinical Staphylococcus aureus isolates resistant to vancomycin. Journal of Bacteriology 2003, 185 : 4638-4643.

Mongodin E, Bajolet O, Cutrona J, Bonnet N, Dupuit F, Puchelle E, de Bentzmann S. Fibronectin-binding proteins of Staphylococcus aureus are involved in adherence to human airway epithelium. Infection and Immunity 2002, 70 : 620-630.

Mongodin E, Bajolet O, Hinnrasky J, Puchelle E, de Bentzmann S. Cell wall-associated protein A as a tool for immunolocalization of Staphylococcus aureus in infected human airway epithelium. Journal of Histochemistry and  Cytochemistry. 2000, 48 : 523-534.

Dupuit F, Gaillard D, Hinnrasky J, Mongodin E, de Bentzmann S, Copreni E, Puchelle E. Differentiated and functional human airway epithelium in tracheal xenografts. American Journal of Physiology (Lung Cellular and Molecular Physiology) 2000, 278 : L165-L176.

Le Prigent K, Lagadic-Gossmann D, Mongodin E, Feuvray D. HCO3- dependant alkalinizing transporter in adult rat ventricular myocytes : characterization and modulation. American Journal of Physiology (Heart Circulation and Physiology) 1997, 42 : H2596 – H2603.

Textbook Chapters and Reviews

Fouts DE, Mongodin EF, Karen E. Nelson. Campylobacter Pathogenomics: From Genomes and Beyond. In: Pathogenomics. M. Pallen (Chief editor), S.R. Gill, K.E. Nelson and G. Preston (Sub-Editors). ASM Press Book, in press.

Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM.  Microbial Biochemistry, Physiology, Ecology and Biotechnology of Hyperthermophilic Thermotoga Species. FEMS Microbiol Rev. 2006, Nov;30(6):872-905.

Nesbo CL, Mongodin EF, Nelson KE, Doolittle WF. The Thermotoga metagenome: lateral gene transfer and recombination. Microbe (formerly known as ASM News), 2006, 1(5), 235-241.

Mongodin EF, Emerson JB and Nelson KE. Microbial Metagenomics. Microbial Metagenomics. A Report on The American Society for Microbiology 105th Annual Meeting, Atlanta GA, June 5-9, 2005. Genome Biology 2005, 2005, 6:347.

Rasko DA and Mongodin EF. A First Decade of Microbial Genomics: what have we learned and where are we going next ? A report on the International Conference on Microbial Genomics; Halifax, Nova Scotia, Canada, April 13-16 205. Genome Biology, 2005, 6:341.

de Bentzmann S, Mongodin E, Plotkowski MC, Puchelle E. Interactions cellules épithéliales respiratoires – bactéries pathogènes. In Biologie et pathologie des épithéliums. C. Clerici, G. Friedlander. Paris : E.D.K., 2000, 213-226.

de Bentzmann S, Mongodin E, Roger P, Puchelle E. Bacterial adherence to airway epithelium. European Respiratory Review 2000, 70 : 125-132.