Jeffrey

Jeffrey Scott McLean , PhD

Associate Professor, Periodontics

Office D-586, Lab D-558

Background

Dr. McLean received his PhD at the University of Southern California and his MSc at the University of Guelph in Canada. Dr. McLean’s research career at the Pacific Northwest National Laboratory, the J. Craig Venter Institute and now at the University of Washington School of Dentistry has been primarily devoted to developing innovative methodologies, tools and new genomic based approaches to study microbial interactions within oral biofilm communities. Currently, he is funded as a PI on multiple active NIH R01 grants that employ generation sequencing techniques such as single cell genomics and metatranscriptomics to characterize the microbial processes that lead to dental caries and maintain the health of the human oral microbiome. Within these projects, one goal is to isolate and capture genomes of oral pathogens and uncultivated novel oral phlya to gain a better understanding of these polymicrobial diseases and pathogen transmission routes.

McLean Research Lab Website

Awards and Recognition

  • Latornell Travel Award
  • National Science and Engineering Research Council (NSERC) Industrial Postgraduate Scholarship
  • Outstanding Performance Award, Scientific contribution to the D.O.E. Genomes to Life Microbial Cell Project
  • Outstanding Performance Award, Dedication and recognition for contributions toward the Microbial Cell Dynamics Laboratory
  • 2 National Laboratory On the Spot Awards for outstanding performance
  • Outstanding Performance Award, Scientific contribution to an ACS article nominated one of top 4 articles of 2007.

Recent Press Articles

Saccharibacteria (2019)

 A Review of TM7 in the Human Oral Microbiome

Culturing TM7 (2018)

UW Health Sciences NewsBeat

Candidate Phylum TM7 and Periodontal Disease (Dec 2014-2015)

Novel genome of recovered from hospital (June 2013)

Single Cell genome of Periodontal Pathogen (2013)

Selected Recent Peer-reviewed Publications

*Corresponding Author #Co-first Author

  1. Bor B, Bedree JK, Shi W, McLean JS, He X.  Saccharibacteria (TM7) in the Human Oral Microbiome. J Dent Res. 2019 Mar 20:22034519831671. doi: 10.1177/0022034519831671. [Epub ahead of print] PubMed PMID: 30894042.
  2. Jain, S., Chang, A.M., Singh, M., McLean, J.S., Coats, S.R., Kramer, R.W. & Darveau, R.P. Identification of PGN_1123 as the gene encoding lipid A deacylase, an enzyme required for Toll-like receptor 4 evasion, in Porphyromonas gingivalis. J Bacteriol (2019). 2019 Feb 19. pii: JB.00683-18. doi: 10.1128/JB.00683-18.
  3. Chang AM, Liu Q, Hajjar AM, Greer A, McLean JS, Darveau Toll-like receptor-2 and -4 responses regulate neutrophil infiltration into the junctional epithelium and significantly contribute to the composition of the oral microbiota. J Periodontol. 2019 Oct;90(10):1202-1212. doi: 10.1002/JPER.18-0719. Epub 2019 Jul 1. PubMed PMID: 31111967; PubMed Central PMCID: PMC6791728
  4. Coats SR, Kantrong N, To TT, Jain S, Genco CA, McLean JS, Darveau RP.  The distinct immune-stimulatory capacities of Porphyromonas gingivalis strains 381 and ATCC 33277 are determined by the fimB allele and gingipain activity. Infect Immun. 2019 Sep 30;. doi: 10.1128/IAI.00319-19. [Epub ahead of print] PubMed PMID: 31570556.
  5. Baker JL, Hendrickson EL, Tang X, Lux R, He X, Edlund A, McLean JS, Shi W.  Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota. Proc Natl Acad Sci U S A. 2019 Apr 11. pii: 201820594. doi: 10.1073/pnas.1820594116. [Epub ahead of print] PubMed PMID: 30975748.
  6. Bor B, McLean JS, Foster KR, Cen L, To TT, Serrato-Guillen A, Dewhirst FE, Shi W, He X.  Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host. Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12277-12282. doi: 10.1073/pnas.1810625115. Epub 2018 Nov 15. PubMed PMID: 30442671
  7. Edlund, A., Yang, Y., Yooseph, S., He, X., Shi, W. & McLean, J.S*. Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation. Microbiome 6, 217 (2018) PMCID: PMC6284299
  8. Bor Batbileg, Jeffrey S. McLean, Kevin R. Foster, Lujia Cen, Thao T. To, Alejandro Serrato-Guillen, Floyd E. Dewhirst, Wenyuan Shi and Xuesong He. Rapid evolution of decreased host susceptibility drives a stable relationship between ultra-small parasite TM7x and its bacterial host. 2018. PNAS In Press Online Week of Nov 12th 2018
  9. Edlund A, Garg N, Mohimani H,Gurevich A, He X, Shi W, Dorrestein PC, McLean JS. 2017. Metabolic fingerprints from the human oral microbiome reveal a vast knowledge gap of secreted small peptidic molecules.
  10. M. Agnello, L. Cen, N.C. Tran, W.Shi, J.S. McLean*, X. He* Arginine Improves pH Homeostasis via Metabolism and Microbiome Modulation. Journal of Dental Research First published date: May-09-2017   10.1177/0022034517707512
  11. To TT, Liu Q, Watling M, Darveau RP, Bumgarner RE, McLean JS. Genome sequence of low-passage clinical isolate Porphyromonas gingivalis MP4-504. Genome Announcements
  12. McLean, J. S.*, Q. Liu, B. Bor, J. K. Bedree, L. Cen, M. Watling, T. T. To, R. E. Bumgarner, X. He and W. Shi (2016). “Draft Genome Sequence of Actinomyces odontolyticus subsp. actinosynbacter Strain XH001, the Basibiont of an Oral TM7 Epibiont.” Genome Announc 4(1).
  13. Guo, L.#, J. S. McLean#, Y. Yang, R. Eckert, C. W. Kaplan, P. Kyme, O. Sheikh, B. Varnum, R. Lux, W. Shi and X. He (2015). “Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology.” Proceedings of the National Academy of Sciences. published ahead of print June 1, 2015, doi:10.1073/pnas.1506207112 Role: #Co-First Author.   OPEN ACCESS
  14. Anna Edlund, Youngik Yang, Shibu Yooseph, Adam P. Hall, Don D. Nguyen, Pieter C. Dorrestein, Karen E. Nelson, Xuesong He, Renate Lux, Wenyuan Shi, Jeffrey S. McLean* Meta-Omics Uncover Temporal Regulation of Pathways Across Oral Microbiome Genera During in vitro Sugar Metabolism. (2105)  International Society for Microbial Ecology Journal (ISME)    OPEN ACCESS
  15. He, Xuesong#, McLean, Jeffrey S.#*(co-first author, co-corresponding author), Edlund, Anna, Yooseph, Shibu, Hall, Adam P., Liu, Su-Yang, Dorrestein, Pieter C., Esquenazi, Eduardo, Hunter, Ryan C., Cheng, Genhong, Nelson, Karen E., Lux, Renate, Shi, Wenyuan. (2015) Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences 112(1):244-249. doi: 10.1073/pnas.1419038112.   OPEN ACCESS
  16. McLean JS* (2014) Advancements toward a systems level understanding of the human oral microbiome. Front Cell Infect Microbiol 4:98. PMCID: MC4114298
  17. Lasken RS & McLean JS (2014) Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15(9):577-584. PMID: 25091868
  18. McLean, JS.* and R. Lasken (2014). “Single cell genomics of bacterial pathogens: outlook for infectious disease research.” Genome Medicine 6(11): 108.
  19. Edlund, A., Yang, Y., Hall, A., Guo, L., Lux, R., He, X., Nelson, K., Nealson, K., Yooseph, S., Shi, W. & McLean, JS*. (2013) An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome. Microbiome 1, 2
  20. McLean, JS*, M.-J. Lombardo, M. G. Ziegler, M. Novotny, J. Yee-Greenbaum, J. H. Badger, G. Tesler, S. Nurk, V. Lesin, D. Brami, A. P. Hall, A. Edlund, L. Z. Allen, S. Durkin, S. Reed, F. Torriani, K. H. Nealson, P. A. Pevzner, R. Friedman, J. C. Venter and R. S. Lasken (2013). “Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.” Genome Research 23(5): 867-877. doi: 10.1101/gr.150433. PMCID: PMC3638142
  21. McLean, JS*, M.-J. Lombardo, J. H. Badger, A. Edlund, M. Novotny, J. Yee-Greenbaum, N. Vyahhi, A. P. Hall, Youngik Yang, C. L. Dupont, M. G. Ziegler, H. Chitsaz, A. E. Allen, S. Yooseph, G. Tesler, P. Pevzner, R. Friedman, K. H. Nealson, J. C. Venter and R. S. Lasken (2013). “Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum.” PNAS. Jun 25;110(26):E2390-9. doi: 10.1073/pnas.1219809110 PMCID: PMC3696752
  22. McLean, JS *, S. J. Fansler, P. D. Majors, K. McAteer, L. Z. Allen, M. E. Shirtliff, R. Lux, W. Shi (2012) Identifying Low pH Active and Lactate-Utilizing Taxa within Oral Microbiome Communities from Healthy Children Using Stable Isotope Probing Techniques. PLoS ONE, 7 (3), e32219. PMCID:PMC3293899
  23. McLean, JS*, O. N. Ona, and P. D. Majors. 2008. Correlated biofilm imaging, transport and metabolism measurements via combined nuclear magnetic resonance and confocal microscopy. ISME J 2:121 – 31.

Additional publications

  1. Bedree Joseph K, Batbileg Bor, Lujia Cen, Anna Edlund, Renate Lux, Jeffrey S. McLean, Wenyuan Shi and   Xuesong He. Quorum Sensing Modulates the Epibiotic-Parasitic Relationship between Actinomyces odontolyticus and its Saccharibacteria epibiont, a Nanosynbacter lyticus strain, TM7x. Microbiol. | doi: 10.3389/fmicb.2018.02049
  2. Daubert D, Pozhitkov A, McLean J, Kotsakis G. Titanium as a modifier of the peri-implant microbiome structure. Clin Implant Dent Relat Res. 2018;1–9.   https://doi.org/10.1111/cid.12676
  3. Baker, J.L., Lindsay, E.L., Faustoferri, R.C., To, T.T., Hendrickson, E.L., He, X., Shi, W., McLean, J.S. & Quivey, R.G., Jr. Characterization of the trehalose utilization operon in Streptococcus mutans reveals that the TreR transcriptional regulator is involved in stress response pathways and toxin production. J Bacteriol (2018). J Bacteriol. 2018 Apr 9. pii: JB.00057-18. doi: 10.1128/JB.00057-18.
  4. Shen, M., Y. Yang, W. Shen, L. Cen, S. McLean, W. Shi, S. Le and X. He (2018). “A Linear Plasmid-Like Prophage of Actinomyces odontolyticus Promotes Biofilm Assembly.” Appl Environ Microbiol 84(17).
  5. Torres PJ, Thompson J, McLean JS, Kelley ST, Edlund A. Discovery of a Novel Periodontal Disease-Associated Bacterium. Microb Ecol. 2018 Jun 2. doi: 10.1007/s00248-018-1200-6. [Epub ahead of print] PubMed PMID: 29860637.
  6. Shi, B., T. Wu, J. McLean, A. Edlund, Y. Young, X. He, H. Lv, X. Zhou, W. Shi, H. Li and R. Lux (2016). “The Denture-Associated Oral Microbiome in Health and Stomatitis.” mSphere 1(6).
  7. Harris, H. W., I. Sanchez-Andrea, S. McLean, E. C. Salas, W. Tran, M. Y. El-Naggar and K. H. Nealson (2017). “Redox Sensing within the Genus Shewanella.” Front Microbiol 8: 2568.
  8. Stanaway, I. B., J. C. Wallace, A. Shojaie, W. C. Griffith, S. Hong, C. S. Wilder, F. H. Green, J. Tsai, M. Knight, T. Workman, E. M. Vigoren, J. S. McLean, B. Thompson and E. M. Faustman (2017). “Human Oral Buccal Microbiomes Are Associated with Farmworker Status and Azinphos-Methyl Agricultural Pesticide Exposure.” Appl Environ Microbiol 83(2).
  9. Wang, M., et al. …. McLean, J. … P. C. Dorrestein and N. Bandeira (2016). “Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.” Nat Biotechnol 34(8): 828-837. Zhong, C., A. Edlund, Y. Yang, J. S. McLean and S. Yooseph (2016). “Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.” PLoS Comput Biol 12(7): e1004991
  10. Bor B, Poweleit N, Bois JS, Cen L, Bedree JK, Zhou ZH, Gunsalus RP, Lux R, McLean JS, He X, Shi W2015. Phenotypic and Physiological Characterization of the Epibiotic Interaction Between TM7x and Its Basibiont Actinomyces. Microb Ecol doi:10.1007/s00248-015-0711-7:1-13.   http://link.springer.com/article/10.1007%2Fs00248-015-0711-7#
  11. Dmitry Antipov, Anton Korobeynikov, Jeffrey S. McLean, and Pavel A. Pevzner. HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads. Bioinformatics first published online November 20, 2015 doi:10.1093/bioinformatics/btv688.  http://bioinformatics.oxfordjournals.org/content/early/2015/11/20/bioinformatics.btv688.short?rss=1
  12. Guo L, McLean JS, Lux R, He X, Shi W2015. The well-coordinated linkage between acidogenicity and aciduricity via insoluble glucans on the surface of Streptococcus mutans. Scientific Reports 5:18015.    http://dx.doi.org/10.1038/srep18015
  13. He, X., McLean, J.S., Guo, L., Lux, R. & Shi, W.(2013). The social structure of a microbial community involved in colonization resistance. ISME J. Online 3 October 2013 doi:10.1038 /ismej.2013.172 PMCID: PMC3930314  https://doi.org/10.1038/ismej.2013.172
  14. Guo, L., W. Hu, X. He, R. Lux, J. McLean and W. Shi (2013). “Investigating Acid Production by Streptococcus mutans with a Surface-Displayed pH-Sensitive Green Fluorescent Protein.” PLoS ONE 8(2): e57182. PMID: 23468929 PMCID: PMC3585301   http://www.plosone.org/article/authors/info%3Adoi%2F10.1371%2Fjournal.pone.0057182
  15. Allen LZ, Ishoey T, Novotny MA, McLean JS, Lasken RS, et al. (2011) Single Virus Genomics: A New Tool for Virus Discovery. PLoS ONE 6(3): e17722. doi:10.1371/journal.pone.0017722 PMID: 21436882 PMCID: PMC3059205 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017722
  16. Tian, Y.; He, X.; Torralba, M.; Yooseph, S.; Nelson, K. E.; Lux, R.; McLean, J. S.; Yu, G.; Shi, W. (2010) Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities. Mol Oral Microbiol, 25 (5), 357-67. PMCID: PMC2951289   http://onlinelibrary.wiley.com/doi/10.1111/j.2041-1014.2010.00585.x/full
  17. McLean, J. S*.; Wanger G, Gorby YA, Wainstein M, McQuaid J, Ishii SI, Bretschger O, Beyenal H, Nealson KH (2010) Quantification of Electron Transfer Rates to a Solid Phase Electron Acceptor through the Stages of Biofilm Formation from Single Cells to Multicellular Communities. Environ Sci Technol 44: 2721-2727. PMID: 20199066  http://pubs.acs.org/doi/abs/10.1021/es903043p McLean, Jeff EST single cell es903043p
  18. McLean, J. S., Pinchuk, G. E., Geydebrekht, O. V., Bilskis, C. L., Zakrajsek, B. A., Hill, E. A., Saffarini, D. A., Romine, M. F., Gorby, Y. A., Fredrickson, J. K., and Beliaev, A. S., 2008. Oxygen-dependent autoaggregation in Shewanella oneidensis MR-1. Environ. Microbiol. Jul;10(7):1861-76. Epub 2008 Apr 10 doi:10.1111/j.1462-2920.2008.01608.x PMID: 18412550  http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2008.01608.x/abstract PDF
  19. McLean, J. S., P. D. Majors, C. L. Reardon, C.L. Bilskis, S.B. Reed, M. F. Romine and J. K. Fredrickson. (2007). “Investigations of structure and metabolism within Shewanella oneidensis MR-1 biofilms.” Journal of Microbiological Methods. 74: 47-56. 10.1016/j.mimet.2008.02.015
  20. Pinchuk, G. E., C. Ammons, D. E. Culley, S. M. Li, J. S. McLean, M. F. Romine, K. H. Nealson, J. K. Fredrickson, and A. S. Beliaev. ( 2007). Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella: Ecological and Physiological Implications for Dissimilatory Metal Reduction. Appl Environ Microbiol. 74(4):1198-208.
  21. Gorby YA, S Yanina, JS McLean, KM Rosso, DM Moyles, A Dohnalkova, TJ Beveridge, I Chang, BH Kim, KS Kim, DE Culley, SB Reed, MF Romine, D Saffarini, EA Hill, L Shi, DA Elias, DW Kennedy, GE Pinchuk, K Watanabe, S Ishii, B Logan, KH Nealson, and JK Fredrickson. (2006). “Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms.” Proceedings of the National Academy of Sciences of the United States of America 103(30):11358-11363.
  22. McLean JS, Beveridge TJ. (2001). Chromate reduction by a pseudomonad isolated from a site contaminated with chromated copper arsenate. Appl Environ Microbiol. Mar; 67(3):1076-84.
  23. McLean JS, Beveridge TJ, Phipps D. (2000). Isolation and characterization of a chromium-reducing bacterium from a chromated copper arsenate-contaminated site. Environ Microbiol. Dec; 2(6):611-9.

Book Chapters

  1. Majors, P.D. and J.S. McLean. (2009). “Dynamic Metabolism Studies of Live Bacterial Films.” in Magnetic Resonance Microscopy. S. L. Codd and J. D. Seymour. Weinheim, Wiley-VCH.   http://dx.doi.org/10.1002/9783527626052 NLM Unique ID: 101511650
  2. McLean J.S., Lee JU, and Beveridge T.J.( 2001). Interactions of Bacteria and Environmental Metals, Fine-Grained Mineral Development and Bioremediation Strategies. In Interactions Between Soil Particles and Microorganisms and Their Impact on the Terrestrial Environment. (Ed. PM Huang) IUPAC Series on Analytical and Physical Chemistry of Environmental Systems. John Wiley and Sons. Ltd., UK.
  3. Mclean, J., T. Beveridge and D. Phipps. (1999) Chromate removal from contaminated groundwater using indigenous bacteria. In Bioremediation of Metals and Inorganic Compounds (Eds. A Leeson and B.C. Alleman). Proceedings of the In Situ and On Site Bioremediation . Fifth International Symposium. April 19-22, , San Diego. California, Battelle Press