Cleber Ouverney

Cleber Ouverney

Duncan Hall, Room 439
Telephone: (408) 924-4806
FAX: (408) 924-4840

Curriculum Vitae [pdf]
Dr. Ouverney's Research Lab 



  • Post-doct, 2005 - Stanford University School of Medicine
    and The Forsyth/Harvard University Dental School
  • Ph.D., 1999 - University of Southern California
  • M.S., 1993 - California State University, East Bay
  • B.S., 1990 - Occidental College


Courses Taught


Research Interests

The focus of the research in my laboratory is to better characterize the diversity of bacteria in natural microbial communities by type and function. Over 99% of environmental microbes are believed to be uncultivable, hence we rely primarily on culture-independent molecular methods to gather information on the composition and role of mixed microbial communities. Some uncultivable bacteria found in environmental samples are also present in humans, and some of those bacteria have been recently associated with human diseases. Our research attempts to discover the natural source of human-associated uncultivable bacteria and to compare the function of those bacteria in their natural environment as well as in the human body. To study function of microbes, we combine in situ hybridization with micro-autoradiography (STARFISH) to determine the types of nutrients a particular bacterium is able to take up without the need of cultivation. Such method may aid in determining more appropriate cultivation media for isolating yet uncultivable bacteria


Selected Publications

Dinis J.M., D.E. Barton, J. Ghadiri, D. Surendar, K. Reddy, F. Velasquez, C.L. Chaffee, M.S. Lee, H. Gavrilova, H. Ozuna, S.A. Smits, and C.C. Ouverney. 2011. In Search of an Uncultured Human- Associated TM7 Bacterium in the Environment. PLoS ONE 6(6): e21280. doi:10.1371/journal.pone.0021280.

Smits S.A. and C.C. Ouverney. 2010. Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective. BMC Bioinformatics, 11(Suppl 6):S18. doi:10.1186/1471-2105-11-S6-S18.

Smits S.A. and C.C. Ouverney. 2010. jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web. PLoS ONE 5(8): e12267. doi: 10.1371/journal.pone.0012267

Marcy, Y., C. Ouverney. E.M. Bik, T. Lösekann, N. Ivanova, H.G. Martin, E. Szeto, D. Platt, P. Hugenholtz, D.A. Relman, S.R. Quake. 2007. Dissecting biological “dark matter” with single-cell genetic analysis of rare uncultivated TM7 microbes from the human mouth. PNAS 104(29): 11889-94.

Jones, B. W., A. Maruyama, C. C. Ouverney, and M. K. Nishiguchi. 2007. Spatial and Temporal Distribution of the Vibrionaceae in Coastal Waters of Hawaii, Australia and France. Microbial Ecology, 54: pp

Ouverney, C. C., G. C. Armitage, and D. A. Relman. 2004. Use of Cloned Artificial Targets for FISH (catFISH) for the optimization of oligonucleotide probe hybridization conditions with 16S rRNA clones for in situ quantification of uncultivated prokayotic cells. In G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, A. D. L Akkermans, and J. D. van Elsas, editors. Molecular Microbial Ecology Manual, 2nd edition. Chapter 3.12: 727-742-169. Kluwer Academic Publishers, Dordrecht.

Ouverney C. C. and J. A. Fuhrman. 2004. Correlating single-cell count with function in mixed natural microbial communities through STARFISH. In G. A. Kowalchuk, F. J. de Bruijn, I. M. Head, A. D. L. Akkermans, and J. D. van Elsas, editors. Molecular Microbial Ecology Manual, 2nd edition. Chapter 8.08: 1689-1710. Kluwer Academic Publishers, Dordrecht

Lepp, P. W., M. M. Brinig, C. C. Ouverney, K. Palm, G. C. Armitage, and D. A. Relman. 2004. Methanogenic Archaea and human periodontal disease. PNAS, 101(16): 6176-6181.

Ouverney, C. C., G. C. Armitage, and D. A. Relman. 2003. Single-cell enumeration of an uncultivated TM7 subgroup in the human subgingival crevice. Applied and Environmental Microbiology, 69 (10): 6294-6298.

Maywald, M., A. Herbay, D. N. Fredricks, C. C. Ouverney, J. C. Kosek, and, D. A. Relman. 2003. Cultivation of Tropheryma whipplei from Cerebrospinal Fluid. J. of Infectious Disease, 188: 801-888.

Brinig, M. M, P. W. Lepp, C. C. Ouverney, G. C. Armitage and D. A. Relman. 2003. Prevalence of Bacteria of Division TM7 in human subgingival plaque and their association with disease. Applied and Environmental Microbiology, 69(3):1687-1694

Ouverney, C. C. and J. A. Fuhrman. 2000. Marine planktonic Archaea take up amino acids. Applied and Environmental Microbiology, 66 (11): 4829-4833

Ouverney, C. C. and J. A. Fuhrman. 1999. Combined microautoradiography-16S rRNA probe technique for the determination of radioisotope uptake by specific microbial cell types in situ. Applied and Environmental Microbiology. 65 (4):1746-1752.

Ouverney. C. C. 1999. Dissecting the Marine bacterioplankton "black box" by type and function through FISH and STARFISH, Ph.D. Dissertation, University of Southern California.

Fuhrman, J. A. and C. C. Ouverney. 1998. Marine microbial diversity studied via 16S rRNA sequences: coastal cloning results and counting of native archaea with fluorescent single cell probes. Aquatic Ecology. 32: 3-5

Ouverney, C. C. and J. A. Fuhrman. 1997. Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramphenicol. Applied and Environmental Microbiology, 63(7): 2735-2740.

Kitting, C. L., C. C. Ouverney, and F. Canabal II. 1993. Small fishes concentrated during the first five years outside an experimental wastewater marsh in San Francisco Bay. Selected proceedings of a Society of Wetland Scientists, Western Chapter. U.C. Davis, CA, March 25-27.

Ouverney, C. C. 1993. Ecology of an Experimental Wastewater Marsh Outflow in South San Francisco Bay. Master's Thesis. California State University, Hayward. 86pp.