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

B.A., 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.
Please see: http://faculty.sites.uci.edu/whitesonlab/publications/

38. Wandro, S., Oliver, A., Gallagher, T., Weihe, C., England, W., Martiny, J., and Whiteson, K. (2019) Predictable molecular adaptation of coevolving Enterococcus faecium and lytic phage EfV12-phi1. Front. Microbiol. (Provisionally Accepted) doi: 10.3389/fmicb.2018.03192

37. Gallagher, T., Phan, J., Oliver, A., Chase, A., England, W., Wandro, S., Hendrickson, C., Riedel, F., Whiteson, K. (2019) Cystic fibrosis-associated Stenotrophomonas maltophilia strain-specific adaptations and responses to pH. Journal of Bacteriology JB.00478-18; DOI: 10.1128/JB.00478-18

36. Lau, W.L., Vaziri, N., Nunes, A., Comeau, A., Langille, M., England, W., Khazaeli, M., Suematsu, Y., Phan, J., and Whiteson, K. (2018) The phosphate binder ferric citrate alters the gut microbiome in rats with chronic kidney disease. Journal of Pharmacology and Experimental Therapeutics jpet.118.251389; DOI: https://doi.org/10.1124/jpet.118.251389

35. Gallagher T, Phan J, Whiteson K. (2018) Getting our fingers on the pulse of slow growing bacteria in hard to reach places. J Bacteriol. pii: JB.00540-18. doi: 10.1128/JB.00540-18.

34. Nusbaum, D., Sun, F., Ren, J., Zhu, Z., Ramsy, N., Pervolarakis, N., Kunde, S., England, W., Gao, B., Fiehn, O., Michail, S., Whiteson, K. (2018) Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients, FEMS Microbiology Ecology, 94:9, fiy133, https://doi.org/10.1093/femsec/fiy133

33. Wandro, S., Osborne, S., Enriquez, C., Bixby, C., Arrieta, A., and Whiteson, K. (2018) The microbiome and metabolome of pre-term infant stool is personalized, and not driven by health outcomes including necrotizing enterocolitis and late-onset sepsis. mSphere 3:e00151-18. PMC5917424.

32. Gao B, Gallagher T, Zhang Y, Elbadawi-Sidhu M, Lai Z, Fiehn O, Whiteson KL. (2018) Tracking polymicrobial metabolism in cystic fibrosis airways: P. aeruginosa metabolism and physiology are influenced by R. mucilaginosa-derived metabolites. mSphere 3:e00151-18. https://doi.org/10.1128/ mSphere.00151-18.

31. Nguyen, C.Q., Thrift, W.J., Bhattacharjee, A., Ranjbar, S., Gallagher, T., Darvishzadeh-Varcheie, M., Sanderson, R.N., Capolino, F., Whiteson, K., Baldi, P., Hochbaum, A., Ragan, R. (2018) Longitudinal Monitoring of Biofilm Formation via Robust Surface-Enhanced Raman Scattering Quantification of Pseudomonas aeruginosa-Produced Metabolites. ACS Appl Mater Interfaces https://doi.org/10.1021/acsami.7b18592

30. Whiteson KL (2018) Vive la persistence: engineering human microbiomes in the 21st century. mSystems3:e00166-17. https://doi.org/10.1128/mSystems.00166-17.

29. Phan J, Gallagher T, Oliver A, England W, Whiteson K. (2018) Fermentation products in the cystic fibrosis airways induce aggregation and dormancy-associated expression profiles in a CF clinical isolate of Pseudomonas aeruginosa FEMS Microbiology Letters, https://doi.org/10.1093/femsle/fny082

28. Wandro S, Carmody L, Gallagher T, LiPuma JJ, Whiteson K. (2017) Making it last: storage time and temperature have differential impacts on metabolite profiles of airway samples from cystic fibrosis patients. mSystems 2:e00100-17. https://doi.org/10.1128/

27. Dutilh, B. E., Reyes, A., Hall, R. J., and Whiteson, K. L. (2017) Editorial: Virus discovery by metagenomics: the (im)possibilities. Front. Microbiol. 8 doi: 10.3389/fmicb.2017.01710

26. Whiteson, K., Agrawal, S., Agrawal, A. (2017) Differential responses of human dendritic cells to metabolites from the oral/airway Microbiome. Clinical and Experimental Immunology 2017 Feb 14. doi: 10.1111/cei.12943. [Epub ahead of print])

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. 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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