Katrine L. Whiteson

Picture of Katrine L. Whiteson
Associate Professor, Molecular Biology and Biochemistry
School of Biological Sciences
Associate Professor, Pediatrics
School of Medicine
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.
Awards and Honors
Chancellor's Fellow, 2022-25
Samueli Integrative Health Scholar, 2022-25
Please see: http://faculty.sites.uci.edu/whitesonlab/publications/
A full list of publications is available from PubMed or Google Scholar

71. Dunham, S., McNair, K., Adams, E., Avelar-Barragan, J., Forner, S., Mapstone, M., Whiteson, K.L. (2022) Longitudinal analysis of the gut microbiome in the 5xfAD mouse model of Alzheimer’s disease bioRxiv 2022.03.02.482725doi: https://doi.org/10.1101/2022.03.02.482725

70. Oliver A, El Alaoui K, Haunschild C, Avelar-Barragan J, Mendez Luque LF, Whiteson K, Fleischman AG. Fecal Microbial Community Composition in Myeloproliferative Neoplasm Patients Is Associated with an Inflammatory State. Microbiol Spectr. 2022 Apr 27:e0003222. doi: 10.1128/spectrum.00032-22. Epub ahead of print. PMID: 35475626.

69. Kumar P, Brazel D, DeRogatis J, Valerin JBG, Whiteson K, Chow WA, Tinoco R, Moyers JT. The cure from within? a review of the microbiome and diet in melanoma. Cancer Metastasis Rev. 2022 Apr 27:1–20. doi: 10.1007/s10555-022-10029-3. Epub ahead of print. PMID: 35474500; PMCID: PMC9042647.

68. Jeney SES, Avelar-Barragan J, Whiteson K, Chang J, Dutta S, Lane F. Fecal Putative Uropathogen Abundance and Antibiotic Resistance Gene Carriage in Women With Refractory Recurrent Urinary Tract Infection Treated With Fecal Microbiota Transplantation. Female Pelvic Med Reconstr Surg. 2022 Apr 1;28(4):213-219. doi: 10.1097/SPV.0000000000001090. Epub 2021 Oct 1. PMID: 34608030.

67. Pfister CA, Light SH, Bohannan B, Schmidt T, Martiny A, Hynson NA, Devkota S, David L, Whiteson K. Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes. mSystems. 2022 Feb 22;7(1):e0137421. doi: 10.1128/msystems.01374-21. Epub 2022 Jan 11. PMID: 35014872; PMCID: PMC8751383.

66. O’Toole GA, Crabbé A, Kümmerli R, LiPuma JJ, Bomberger JM, Davies JC, Limoli D, Phelan VV, Bliska JB, DePas WH, Dietrich LE, Hampton TH, Hunter R, Khursigara CM, Price-Whelan A, Ashare A, Cramer RA, Goldberg JB, Harrison F, Hogan DA, Henson MA, Madden DR, Mayers JR, Nadell C, Newman D, Prince A, Rivett DW, Schwartzman JD, Schultz D, Sheppard DC, Smyth AR, Spero MA, Stanton BA, Turner PE, van der Gast C, Whelan FJ, Whitaker R, Whiteson K. Model Systems to Study the Chronic, Polymicrobial Infections in Cystic Fibrosis: Current Approaches and Exploring Future Directions. mBio. 2021 Oct 26;12(5):e0176321. doi: 10.1128/mBio.01763-21. Epub 2021 Sep 21. PMID: 34544277; PMCID: PMC8546538.

65. Vieira J, Gallagher T, Sui HY, Jesudasen S, Whiteson K, O’Toole GA, Hanselmann K, Lai PS. Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome. J Vis Exp. 2021 Aug 3;(174). doi: 10.3791/62888. PMID: 34424248.

64. Albright MBN, Louca S, Winkler DE, Feeser KL, Haig SJ,Whiteson KL, Emerson JB, Dunbar J. Solutions in microbiome engineering: prioritizing barriers to organism establishment. ISME J. 2021 Aug 21;. doi: 10.1038/s41396-021-01088-5. [Epub ahead of print] Review. PubMed PMID: 34420034.

63. Vieira J, Gallagher T, Sui HY, Jesudasen S,Whiteson K, O’Toole GA, Hanselmann K, Lai PS. Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome. J Vis Exp. 2021 Aug 3;(174). doi: 10.3791/62888. PubMed PMID: 34424248.

62. Avelar-Barragan, J., DeDecker, L., Lu, Z., Coppedge, B., Karnes, W.E.,Whiteson, K.L., 2021. Distinct Colon Mucosa Microbiomes associated with Tubular Adenomas and Serrated Polyps. bioRxiv 2021.07.20.453135. https://doi.org/10.1101/2021.07.20.453135(Under review at Nature Biofilms and Microbiomes)

61. Rothman, J.A., Loveless, T.B., Kapcia, J., Adams, E.D., Steele, J.A., Zimmer-Faust, A.G., Langlois, K., Wanless, D., Griffith, M., Mao, L., Chokry, J., Griffith, J.F.,Whiteson, K.L.,2021. RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants. Appl Environ Microbiol. 2021 Sep 22:AEM0144821. doi: 10.1128/AEM.01448-21

60. Neerincx AH,Whiteson K, Phan JL, Brinkman P, Abdel-Aziz MI, Weersink EJM, Altenburg J, Majoor CJ, Maitland-van der Zee AH, Bos LDJ. Lumacaftor/ivacaftor changes the lung microbiome and metabolome in cystic fibrosis patients. ERJ Open Res. 2021 Apr;7(2). doi: 10.1183/23120541.00731-2020. eCollection 2021 Apr. PubMed PMID: 33898610; PubMed Central PMCID: PMC8053817.

59. Oliver A, Chase AB, Weihe C, Orchanian SB, Riedel SF, Hendrickson CL, Lay M, Sewall JM, Martiny JBH, Whiteson K. High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids. mSystems. 2021 Mar 16;6(2):e00115-21. doi: 10.1128/mSystems.00115-21. PMID: 33727392.

58. Wandro, S., Ghatbale, P., Attai, H., Hendrickson, C., Samillano, C., Suh, J., Pride, D.T., Whiteson, K. Phage Cocktails can prevent the evolution of phage-resistant Enterococcus bioRxiv 2021.01.27.428553 (Accepted at mSystems)

57. Phan, J., Kapcia, J. III, Rodriguez C.I., Vogel, V., Dunham., S.J.B., Whiteson, K. Capturing actively produced microbial volatile organic compounds from human associated samples with vacuum assisted sorbent extraction bioRxiv 2021.02.16.431476; doi: https://doi.org/10.1101/2021.02.16.431476 (Accepted at the Journal of Visualized Experimentation)

56. Jeney SES, Lane F, Oliver A, Whiteson K, Dutta S. Fecal Microbiota Transplantation for the Treatment of Refractory Recurrent Urinary Tract Infection. Obstet Gynecol. 2020 Oct;136(4):771-773. doi: 10.1097/AOG.0000000000004052. PMID: 32925627.

55. DeDecker L, Coppedge B, Avelar-Barragan J, Karnes W, Whiteson K. Microbiome distinctions between the CRC carcinogenic pathways. Gut Microbes. 2021 Jan 15:1-12. doi: 10.1080/19490976.2020.1854641. Epub ahead of print. PMID: 33446008.

54. Zhang Y, Gao B, Valdiviez L, Zhu C, Gallagher T, Whiteson K, Fiehn O. Comparing Stable Isotope Enrichment by Gas Chromatography with Time-of-Flight, Quadrupole Time-of-Flight, and Quadrupole Mass Spectrometry. Anal Chem. 2021 Feb 2;93(4):2174-2182. doi: 10.1021/acs.analchem.0c04013. Epub 2021 Jan 12. PMID: 33434014.

53. Adams, E., Gille, A., Alaniz N., Jamie, C., Patton, J., Whiteson, K. (2020) Comparing Fecal, Saliva, and Chicha Microbiomes Between Mothers and Children in an Indigenous Ecuadorian Cohort bioRxiv 2020.10.02.323097; doi: https://doi.org/10.1101/2020.10.02.323097

53a. Related protocol: Eric Adams, Stephen Wandro, Julio Avelar-Barragan, Andrew Oliver, Katrine Whiteson 2020. Low Volume Methodology for Nextera DNA Flex Library Prep Kit (96 Samples). protocols.iohttps://protocols.io/view/low-volume-methodology-for-nextera-dna-flex-librar-be6rjhd6

52. Microbiome Centers Consortium COVID Committee. Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus. mSystems. 2020 Dec 1;5(6):e00999-20. doi: 10.1128/mSystems.00999-20. PMID: 33262241; PMCID: PMC7716391.

51. Phan J, Ranjbar S, Kagawa M, Gargus M, Hochbaum AI, Whiteson KL. Thriving Under Stress: Pseudomonas aeruginosa Outcompetes the Background Polymicrobial Community Under Treatment Conditions in a Novel Chronic Wound Model. Front Cell Infect Microbiol. 2020 Oct 6;10:569685. doi: 10.3389/fcimb.2020.569685. PMID: 33123495; PMCID: PMC7573134.

50.Gallagher T, Riedel S, Kapcia J, Caverly LJ, Carmody L, Kalikin LM, Lu J, Phan J, Gargus M, Kagawa M, Leemans SW, Rothman JA, Grun F, LiPuma JJ, Whiteson KL. LC-MS detection of antibiotic agents in sputum from persons with cystic fibrosis. Antimicrob Agents Chemother. 2020 Nov 2:AAC.00927-20. doi: 10.1128/AAC.00927-20. Epub ahead of print. PMID: 33139284.

49. Rothman JA, Loveless TB, Griffith ML, Steele JA, Griffith JF, Whiteson KL. Metagenomics of Wastewater Influent from Southern California Wastewater Treatment Facilities in the Era of COVID-19. Microbiol Resour Announc. 2020 Oct 8;9(41):e00907-20. doi: 10.1128/MRA.00907-20. PMID: 33033132; PMCID: PMC7545286.

48. Oliver A, LaMere B, Weihe C, Wandro S, Lindsay KL, Wadhwa PD, Mills DA, Pride D, Fiehn O, Northen T, de Raad M, Li H, Martiny JBH, Lynch S, Whiteson K. Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy. mBio Aug 2020, 11 (4) e01851-20; PMID: 32843557

47. Sewall JM, Oliver A, Denaro K, Chase AB, Weihe C, Lay M, Martiny JBH, Whiteson K. Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course. J Microbiol Biol Educ. 2020 Apr 30;21(1):21.1.40. doi: 10.1128/jmbe.v21i1.1991. eCollection 2020. PMID: 32431776

46. Maughan H., Whiteson K. (2020) Saliva as a Window into the Human Oral Microbiome and Metabolome. In: Granger D., Taylor M. (eds) Salivary Bioscience. Springer, Cham. https://doi.org/10.1007/978-3-030-35784-9_7

45. Hahn A, Whiteson K, Davis TJ, Phan J, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Bean HD. Longitudinal Associations of the Cystic Fibrosis Airway Microbiome and Volatile Metabolites: A Case Study. Front Cell Infect Microbiol. 2020 Apr 28;10:174. doi: 10.3389/fcimb.2020.00174. eCollection 2020. PMID: 32411616

44. Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer. 2020 Mar;6(3):192-204. doi: 10.1016/j.trecan.2020.01.004. Epub 2020 Feb 7.
PMID: 32101723 Review.

43. Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. The emergence of microbiome centres. Nat Microbiol. 2020 Jan;5(1):2-3. doi: 10.1038/s41564-019-0644-x. PMID: 31857734

42. Bru JL, Rawson B, Trinh C, Whiteson K, Høyland-Kroghsbo NM, Siryaporn A. PQS Produced by the Pseudomonas aeruginosa Stress Response Repels Swarms Away from Bacteriophage and Antibiotics. J Bacteriol. 2019 Nov 5;201(23):e00383-19. doi: 10.1128/JB.00383-19. Print 2019 Dec PMID: 31451543 Free PMC article.

41. Rhoades N, Barr T, Hendrickson S, Prongay K, Haertel A, Gill L, Garzel L, Whiteson K, Slifka M, Messaoudi I. Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease. Genome Biol. 2019 Aug 26;20(1):173. doi: 10.1186/s13059-019-1789-x. PMID: 31451108 Free PMC article.

40. Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O’Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol. 2019 Oct;4(10):1727-1736. doi: 10.1038/s41564-019-0494-6. Epub 2019 Jul 8. PMID: 31285584

39. Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17. PMID: 30556814; PMCID: PMC6871006.
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
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