A full list of publications is available from PubMed or Google Scholar
UCI ‘Fiber Force’ Study Finds High-fiber Diet Brings Significant Changes to Human Gut Microbiome
UCI researchers monitor SARS-CoV-2 using wastewater-based epidemiology
Cystic Fibrosis Foundation Funds Multi-UC Bacteriophage Research Project
A full list of publications is available from PubMed or Google Scholar
2024
86. Dunham, S.J.B., Avelar-Barragan, J., Rothman, J.A., Adams, E.D., Faraci, G., Forner, S., Kawauchi, S., Tenner, A.J., Greene, K., LaFerla, F., MacGregor, G., Mapstone, M., & Whitney, K.L. (Year). Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in (hAβ-KI) mice. Alzheimer’s and Dementia, Accepted February 2024
85. Mendez Luque LF, Avelar-Barragan J, Nguyen H, Nguyen J, Soyfer EM, Liu J, Chen JH, Mehrotra N, Huang X, Kosiorek HE, Dueck A, Himstead A, Heide E, Lem M, El Alaoui K, Mas E, Scherber RM, Mesa RA, Whiteson KL, Odegaard A, Fleischman AG. The NUTRIENT Trial (NUTRitional Intervention among myEloproliferative Neoplasms): Results from a Randomized Phase I Pilot Study for Feasibility and Adherence. Cancer Res Commun. 2024 Mar 5;4(3):660-670. doi: 10.1158/2767-9764.CRC-23-0380. PMID: 38391189; PMCID: PMC10913729.
84. Routy B, Jackson T, Mählmann L, Baumgartner CK, Blaser M, Byrd A, Corvaia N, Couts K, Davar D, Derosa L, Hang HC, Hospers G, Isaksen M, Kroemer G, Malard F, McCoy KD, Meisel M, Pal S, Ronai Z, Segal E, Sepich-Poore GD, Shaikh F, Sweis RF, Trinchieri G, van den Brink M, Weersma RK, Whiteson K, Zhao L, McQuade J, Zarour H, Zitvogel L. Melanoma and microbiota: Current understanding and future directions. Cancer Cell. 2024 Jan 8;42(1):16-34. doi: 10.1016/j.ccell.2023.12.003. Epub 2023 Dec 28. PMID: 38157864.
2023
83. Bru JL, Kasallis SJ, Chang R, Zhuo Q, Nguyen J, Pham P, Warren E, Whiteson K, Høyland-Kroghsbo NM, Limoli DH, Siryaporn A. The great divide: rhamnolipids mediate separation between P. aeruginosaand S. aureus. Front Cell Infect Microbiol. 2023 Sep 15;13:1245874. doi: 10.3389/fcimb.2023.1245874. PMID: 37780859; PMCID: PMC10540625.
82. Petrisko TJ, Gargus M, Chu SH, Selvan P, Whiteson KL, Tenner AJ. Influence of complement protein C1q or complement receptor C5aR1 on gut microbiota composition in wildtype and Alzheimer’s mouse models. J Neuroinflammation. 2023 Sep 19;20(1):211. doi: 10.1186/s12974-023-02885-9. PMID: 37726739; PMCID: PMC10507976.
81. Khong E, Oh J, Jimenez JM, Liu R, Dunham S, Monsibais A, Rhoads A, Ghatbale P, Garcia A, Cobián Güemes AG, Blanc AN, Chiu M, Kuo P, Proost M, Kline A, Aslam S, Schooley RT, Whiteson K, Fraley SI, Pride DT. A simple solid media assay for detection of synergy between bacteriophages and antibiotics. bioRxiv [Preprint]. 2023 Aug 24:2023.08.23.554535. doi: 10.1101/2023.08.23.554535. PMID: 37662290; PMCID: PMC10473724. Accepted Spectrum
80. Avelar-Barragan J, Mendez Luque LF, Nguyen J, Nguyen H, Odegaard AO, Fleischman AG, Whiteson KL. Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention. mBio. 2023 Oct 25:e0230823. doi: 10.1128/mbio.02308-23. Epub ahead of print. PMID: 37877698.
79. Rothman JA, Saghir A, Zimmer-Faust AG, Langlois K, Steele JA, Griffith JF, Whiteson KL. Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater from April 2020 – August 2021. medRxiv. 2023 Apr 14. doi: https://doi.org/10.1101/2023.04.14.23288559
78. Rothman JA, Riis JL, Hamilton KR, Blair C, Granger DA, Whiteson KL. Oral microbial communities in children, caregivers, and associations with salivary biomeasures and environmental tobacco smoke exposure. mSystems. 2023 Jun 20:e0003623. doi: 10.1128/msystems.00036-23. PMID: 37338237.
77. Green SI, Clark JR, Santos HH, Weesner KE, Salazar KC, Aslam S, Campbell WJ, Doernberg SB, Blodget E, Morris MI, Suh GA, Obeid K, Silveira FP, Filippov AA, Whiteson KL, Trautner BW, Terwilliger AL, Maresso A. A retrospective, observational study of 12 cases of expanded access customized phage therapy: production, characteristics, and clinical outcomes. Clin Infect Dis. 2023 Jun 3:ciad335. doi: 10.1093/cid/ciad335. Online ahead of print. PMID: 37279523.
76. Zünd M, Dunham SJB, Rothman JA, Whiteson KL. What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology. mSystems. 2023 Feb 23;8(1):e0080722. doi: 10.1128/msystems.00807-22. Epub 2023 Jan 18. PMID: 36651762 Free PMC article. Review.
75. Rothman JA, Saghir A, Chung SA, Boyajian N, Dinh T, Kim J, Oval J, Sharavanan V, York C, Zimmer-Faust AG, Langlois K, Steele JA, Griffith JF, Whiteson KL. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes. Water Res. 2023 Feb 1;229:119421. doi: 10.1016/j.watres.2022.119421. Epub 2022 Nov 24. PMID: 36455460.
2022
74. Rothman J, Whiteson, KL Sequencing and variant detection of eight abundant plant-infecting tobamoviruses across Southern California wastewater; Microbiol Spectr10:e03050-22. https://doi.org/10.1128/spectrum.03050-22
73. Avelar-Barragan J, DeDecker L, Lu ZN, Coppedge B, Karnes WE, Whiteson KL. Distinct colon mucosa microbiomes associated with tubular adenomas and serrated polyps. NPJ Biofilms Microbiomes. 2022 Aug 29;8(1):69. doi: 10.1038/s41522-022-00328-6. PMID: 36038569; PMCID: PMC9424272.
72. Wandro S, Ghatbale P, Attai H, Hendrickson C, Samillano C, Suh J, Dunham SJB, Pride DT, Whiteson K. Phage Cocktails Constrain the Growth of Enterococcus. mSystems. 2022 Aug 30;7(4):e0001922. doi: 10.1128/msystems.00019-22. Epub 2022 Jun 28. PMID: 35762793; PMCID: PMC9426582.
71. Vieira J, Jesudasen S, Bringhurst L, Sui HY, McIver L, Whiteson K, Hanselmann K, O’Toole GA, Richards CJ, Sicilian L, Neuringer I, Lai PS. Supplemental Oxygen Alters the Airway Microbiome in Cystic Fibrosis. mSystems. 2022 Aug 24:e0036422. doi: 10.1128/msystems.00364-22. Epub ahead of print. PMID: 36000724.
70. Jiang, S.C.; Bischel, H.N.; Goel, R.; Rosso, D.; Sherchan, S.P.; Whiteson, KL; Yan, T.; Solo-Gabriele, H.M. Integrating Virus Monitoring Strategies for Safe Non-Potable Water Reuse. Water 2022, 14, 1187. https://doi.org/10.3390/w14081187
69. Dunham SJB, McNair KA, Adams ED, Avelar-Barragan J, Forner S, Mapstone M, Whiteson KL. Longitudinal Analysis of the Microbiome and Metabolome in the 5xfAD Mouse Model of Alzheimer’s Disease. mBio. 2022 Dec 20;13(6):e0179422. doi: 10.1128/mbio.01794-22. Epub 2022 Dec 5. PMID: 36468884; PMCID: PMC9765021.
68. 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. (lead author A. Oliver is a Whiteson lab PhD student who defended in June 2021)
67. 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.
66. 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.
65. Phan, J., Kapcia III, J., Rodriguez, C. I., Vogel, V. L., Cardin, D. B., Dunham, S. J. B., Whiteson, K. Capturing Actively Produced Microbial Volatile Organic Compounds from Human-Associated Samples with Vacuum-Assisted Sorbent Extraction. J. Vis. Exp. (184), e62547, doi:10.3791/62547 (2022).
64. 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.
2021
63. 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.
62. 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.
61. 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.
60. 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.
59. 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
58. 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.
57. 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. **Editors Pick
2020
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.io https://protocols.io/view/low-volume-methodology-for-nextera-dna-flex-librar-be6rjhd6 **Featured, October 2020
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 J, Griffith J, Griffith M, Steele J, Whiteson KL. Metagenomics of wastewater influent from Southern California wastewater treatment facilities in the era of COVID-19. *accepted at Microbiology Resource Announcements, September 18, 2020
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
2019
42. Bru, JL, , Rawson, B, Trinh, C, Whiteson, K, Høyland-Kroghsbo, NM, Siryaporn, A. (2019) PQS produced by the Pseudomonas aeruginosastress response repels swarms away from bacteriophage and antibiotics Journal of Bacteriology Aug 2019, JB.00383-19; DOI: 10.1128/JB.00383-19.
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 Biology. 2019 Aug 26;20(1):173.
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 Jul 8;. doi: 10.1038/s41564-019-0494-6. [Epub ahead of print] PubMed PMID: 31285584.
39. 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. doi: 10.3389/fmicb.2018.03192
38. Gallagher, T., Phan, J., Oliver, A., Chase, A., England, W., Wandro, S., Hendrickson, C., Riedel, F., Whiteson, K. (2019) Cystic fibrosis-associated Stenotrophomonas maltophiliastrain-specific adaptations and responses to pH. Journal of Bacteriology 201(7). JB.00478-18; DOI: 10.1128/JB.00478-18 PMCID: PMC6416904.
2018
37. 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. 2018 Dec 17;. doi: 10.1038/nbt.4306. [Epub ahead of print] PubMed PMID: 30556814.
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
2017
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. doi: 10.1088/1752-7163/aa5833.
2016
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]
20. Quinn, R. A., Whiteson, K., Lim, Y.W., Salamon, P., Bailey, B., Mienardi, S., Sanchez, S. E., Blake, D., Conrad, D., 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.
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.
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.
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. highlighted in several news articles and blogs: Molloy, S. A metabolic milieu. Nature Reviews Microbiology 12, 315 (2014);
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. 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. 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.
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.
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.
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. * 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.
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.
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.
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. * 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.
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, 121–129.1
1. Grindley, N.D.F., Whiteson, K.L., Rice, P.A. (2006). Mechanisms of site-specific recombination. Annu. Rev. Biochem. 75, 567–605.
