Katrine L. Whiteson

picture of Katrine L. Whiteson

Assistant Professor, Molecular Biology and Biochemistry
School of Biological Sciences
Assistant Professor, Pediatrics
School of Medicine
Associate Director, UCI Microbiome Initiative

A.B., University of California, Berkeley, 2000, Molecular Cell Biology - Biochemistry

Ph.D., University of Chicago, 2007, Biochemistry

Phone: (949) 824-9032
Email: katrine@uci.edu

University of California, Irvine
3236 McGaugh Hall
Mail Code: 3900
Irvine, CA 92697
Research Interests
host-associated microbial communities, metabolomics, metagenomics, microbial ecology, phage, fermentation, polymicrobial infection, microbial interactions, human microbiome
August 2008 – August 2011 Research Scientist, (30% time) University of Geneva (Prof. Jacques Schrenzel,MD and Prof. Patrice Francois, PhD, Genomic Research Lab)

Sept. 2011- August 2014 Post-doc/Adjunct Faculty, San Diego State University (Prof. Forest Rohwer, PhD)
Research Abstract
I am a biochemist interested in human associated microbial and viral communities. I use metagenomics, metabolomics, microbial genetics and ecological statistics to answer questions about how microbes and viruses affect human health. I am interested in understanding how individual and persistent human-associated microbial and viral communities affect health. Infection with a bacterial pathogen, vaccination, immune development and even taking a Tylenol does not occur in a vacuum. Dynamic microbial and viral communities constantly inhabit our bodies, encoding the majority of the unique genes that alter these processes. Resident microbial and viral community composition is unique to each human.

Specifically, I am working to understand the role of persistent microbial colonization in triggering inflammatory episodes in Cystic Fibrosis patients. Understanding microbial interactions and changes in microbial physiology that are associated with changes in patient status may lead to the development of biomarkers to diagnose changes in infection earlier and more specifically.

I am also interested in how phage shape dynamic host-associated microbial communities, and in characterizing the function of the 70% of phage encoded genes with no known function.
Preprint: Wandro, S., Osborne, S., Enriquez, C., Bixby, C., Arrieta, A., and Whiteson, K. (2017) Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants. bioRxiv 125922.
Please see: http://faculty.sites.uci.edu/whitesonlab/publications/

25. Phan, J., Meinardi, S., Barletta, B., Blake, D., and Whiteson, K. (2017) Stable isotope profiles reveal active production of VOCs from human-associated microbes. Journal of Breath Research (accepted).

24. Bos, L. D. J., Meinardi, S., Blake, D., and Whiteson, K. (2016) Bacteria in the airways of patients with cystic fibrosis are genetically capable of producing VOCs in breath. J. Breath Res. 10, 047103. http://iopscience.iop.org/article/10.1088/1752-7163/10/4/047103/meta

23. Quinn, R. A., Whiteson, K., Lim, Y. W., Zhao, J., Conrad, D., LiPuma, J. J., Rohwer, F., and Widder, S. (2016) Ecological networking of cystic fibrosis lung infections. npj Biofilms and Microbiomes 2, 4. http://www.nature.com/articles/s41522-016-0002-1

22. Quinn, R. A., Lim, Y. W., Mak, T. D., Whiteson, K., Furlan, M., Conrad, D., Rohwer, F., and Dorrestein, P. (2016) Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease. PeerJ 4, e2174. https://peerj.com/articles/2174/

21. Quinn, R. A., Phelan, V. V., Whiteson, K., Garg, N., Bailey, B. A., Lim, Y. W., Conrad, D. J., Dorrestein, P. C., and Rohwer, F. L. (2015) Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. ISME J. 10.1038/ismej.2015.207 [Epub ahead of print] http://www.nature.com/ismej/journal/v10/n6/full/ismej2015207a.html

20. Quinn, R.A, Whiteson, K., Lim, Y.W., Conrad, D., Candido, A., Salamon, P., and Rohwer, F. (2015) A Winogradsky-Based Culture System Shows an Association between Microbial Fermentation and Cystic Fibrosis Exacerbation. ISME Journal. 9(4):1024-38. http://www.nature.com/ismej/journal/v9/n4/full/ismej2014266a.html

19. Whiteson K.L., Lazarevic V., Tangomo M., Girard M., Francois P., Schrenzel J. and the GESNOMA study group (2014). NOMA affected children from Niger have distinct oral microbial communities. Plos Neglected Tropical Disease, 8(12):e3240. http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0003240

18. Whiteson, K., Bailey, B., Bergkessel, M., Conrad, D., Delhaes, L., Felts, B., J. Kirk Harris, R. Hunter, Y.W. Lim, H. Maughan, R. Quinn, P. Salamon, J. Sullivan, B.D. Wagner, P.B. Rainey (2014). The upper respiratory tract as a microbial source for pulmonary infections: Parallels from Island Biogeography. Am J Respir Crit Care Med. 189(11):1309-15. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098084/

17. Quinn, R.A., Hester, E., Lim, Y.W. , Conrad, D., Rohwer, F., and Whiteson, K. (2014) Biogeochemical forces shape the composition and physiology of polymicrobial communities in the Cystic Fibrosis lung. mBio 18;5(2):e00956-13. http://mbio.asm.org/cgi/pmidlookup?view=long&pmid=24643867 *** highlighted in several news articles and blogs: Molloy, S. A metabolic milieu. Nature Reviews Microbiology 12, 315 (2014); *** http://www.altmetric.com/details.php?citation_id=2195399

16. Whiteson, K., Meinardi, S., Lim, Y.W., Schmieder, R., Quinn, R., Maughan, H., Blake, D.R., Conrad, D., Rohwer, F. 2014 Breath gas metabolites and bacterial metagenomes from Cystic Fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. ISMEJ 8, 1247–1258. http://www.nature.com/ismej/journal/v8/n6/full/ismej2013229a.html *** highlighted in several news articles and blogs: http://www.altmetric.com/details.php?citation_id=2042954

15. Whiteson, K., Hernandez, D., Lazarevic, L., Gaia, N., Farinelli, F., François, P., Pilo, P., Frey, J., Schrenzel, J. (2014) A genomic perspective on a new bacterial genus and species from the Alcaligenaceae family, Basilea psittacopulmonis DSM 24701. BMC Genomics 15:169. *** highly accessed

14. Barr, J. J., Auro, R., Furlan, M., Whiteson, K. L., Erb, M. L., Pogliano, J., Stotland, A., Wolkowicz, R., Cutting, A. S., Doran, K. S., Salamon, P., Youle, M., and Rohwer, F. (2013) Bacteriophage adhering to mucus provide a non–host-derived immunity. PNAS 110, 10771–10776. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=23690590 Highlighted in: *** Meyer, J. R. (2013) Sticky bacteriophage protect animal cells. Proc. Natl. Acad. Sci. U.S.A. 110, 10475–10476. *** Wootton, L. (2013) Phage biology: A new barrier at mucosal surfaces. Nat. Rev. Microbiol. 11, 430–431. *** Microbiomics: A virus shield. The Economist, May 25, 2013. *** Friendly Viruses Protect Us Against Bacteria. Science, May 20, 2013. *** Yong, E. (2013) Viruses in the gut protect from infection. Nature. *** Zimmer, C. (2013) Meet Your New Symbionts: Trillions of Viruses. National Geographic *** Zielinska, E. (2013) Protective Phages Viruses that attack bacteria may be an important component of our gut microbiota. The Scientist

13. Lazarevic, V., Manzano, S., Gaia, N., Girard, M., Whiteson, K., Hibbs, J., Francois, P., Gervaix, A., and Schrenzel, J. (2013) Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media. Clin Microbiol Infect 19: E335–E342. http://www.sciencedirect.com/science/article/pii/S1198743X14614336

12. Lim, Y. W., Schmieder, R., Haynes, M., Furlan, M., Matthews, T. D., Whiteson, K., Poole, S. J., Hayes, C. S., Low, D. A., Maughan, H., Edwards, R., Conrad, D., and Rohwer, F. (2013) Mechanistic Model of Rothia mucilaginosa Adaptation toward Persistence in the CF Lung, Based on a Genome Reconstructed from Metagenomic Data. PLoS ONE 8, e64285. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064285

11. Reyes, A., Semenkovich, N.P., Whiteson, K., Rohwer, F., Gordon, J.I. (2012) Going viral: next-generation sequencing applied to phage populations in the human gut. Nat. Rev. Microbiol. 10, 607–617. http://www.nature.com/nrmicro/journal/v10/n9/full/nrmicro2853.html

10. Bolivar, I.*, Whiteson, K.*, Stadelmann, B., Baratti-Mayer, D., Gizard, Y., Mombelli, A., Pittet, D., Schrenzel, J., 2012. Bacterial diversity in oral samples of children in Niger with acute NOMA, acute necrotizing gingivitis, and healthy controls. PLoS Negl Trop Dis 6, e1556. http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0001556
* contributed equally

9. Fischer, A., Whiteson, K., Lazarevic, V., Hibbs, J., Francois, P., Schrenzel, J. (2012) Infant gut microbial colonization and health: recent findings from metagenomics studies. Journal of Integrated OMICS.

8. Lazarevic, V., Whiteson, K., Gaïa, N., Gizard, Y., Hernandez, D., Farinelli, L., Osterås, M., François, P., Schrenzel, J. (2012). Analysis of the salivary microbiome using culture-independent techniques. J Clin Bioinformatics 2, 4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296672/

7. Stenz, L., Francois, P., Whiteson, K., Wolz, C., Linder, P., Schrenzel, J. (2011). The CodY pleiotropic repressor controls virulence in gram-positive pathogens. FEMS Immunol. Med. Microbiol. 62, 123–139. http://femsim.oxfordjournals.org/content/62/2/123.long

6. Lazarevic, V., Whiteson, K., François, P., Schrenzel, J. (2010). The salivary microbiome, assessed by a high-throughput and culture-independent approach. Journal of Integrated OMICS 1, 28–35.

5. Lazarevic, V., Whiteson, K., Hernandez, D., François, P., Schrenzel, J. (2010). Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 11, 523. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-523

4. Lazarevic, V.*, Whiteson, K.*, Huse, S., Hernandez, D., Farinelli, L., Osterås, M., Schrenzel, J., François, P. (2009). Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 79, 266–271. http://www.sciencedirect.com/science/article/pii/S0167701209002966
* contributed equally ** Top 25 hottest articles, #1, October – December 2009

3. Whiteson, K.L., Rice, P.A. (2008). Binding and catalytic contributions to site recognition by flp recombinase. J. Biol. Chem. 283, 11414–11423. http://www.jbc.org/content/283/17/11414.long

2. Whiteson, K.L., Chen, Y., Chopra, N., Raymond, A.C., Rice, P.A. (2007). Identification of a potential general acid/base in the reversible phosphoryl transfer reactions catalyzed by tyrosine recombinases: Flp H305. Chem. Biol. 14, 121–129. http://www.sciencedirect.com/science/article/pii/S1074552107000397

1. Grindley, N.D.F., Whiteson, K.L., Rice, P.A. (2006). Mechanisms of site-specific recombination. Annu. Rev. Biochem. 75, 567–605.


Whiteson K.L., Lazarevic V., Tangomo M., Girard M., Francois P., Schrenzel J. Shared human oral microbial community structure in co-habiting family members.

Whiteson K. Human Disease at a Molecular Level. Contract with Garland Science; undergraduate textbook in preparation, six of nine chapters have been reviewed by professors of relevant courses
Graduate Programs
Cellular and Molecular Biosciences

Research Center
Center for Viral Research
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