Publications

Recent Press Articles

 

Science News

Immune-regulating drug improves gum disease in mice

Date: April 28, 2020

https://www.sciencedaily.com/releases/2020/04/200428112540.htm

 

News items

NEWS RELEASE 8-APR-2019
Oral bacteria ‘battle royale’ helps explain how a pathogen causes hospital infections
Quote by McLean

https://www.eurekalert.org/pub_releases/2019-04/fi-ob040819.php

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)

UW Health Sciences NewsBeat

EurekAlert!

Science Daily

Novel genome of recovered from hospital (June 2013)

Science News from the Journal of Science

Single Cell genome of Periodontal Pathogen (2013)

San Diego Union Tribune


Selected Recent Peer-Reviewed Publications

*Corresponding Author #Co-first Author


2020

Bor B, Collins AJ, Murugkar PP, Balasubramanian S, To TT, Hendrickson EL, Bedree JK, Bidlack FB, Johnston CD, Shi W, McLean JS, He X, Dewhirst FE. Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts. J Dent Res. 2020 Feb https://doi.org/10.1177/0022034520905792. PubMed PMID: 32075512.

Jonathan Y An, Kristopher A Kerns, Andrew Ouellette, Laura Robinson, H Douglas Morris, Catherine Kaczorowski, So-Il Park, Title Mekvanich, Alex Kang, Jeffrey S McLean, Timothy C Cox, Matt Kaeberlein. Rapamycin rejuvenates oral health in aging mice. eLife, 2020; 9

https://elifesciences.org/articles/54318

2019 

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.

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.

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

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 Immun2019 Sep 30;. doi: 10.1128/IAI.00319-19. [Epub ahead of print] PubMed PMID: 31570556.

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.

 

2018

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

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

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

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. mSystems 2:e00058-17.

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

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

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).

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.1506207112Role: #Co-First Author. http://www.pnas.org/content/early/2015/05/27/1506207112.abstract OPEN ACCESS

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) http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201572a.html OPEN ACCESS

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. http://www.pnas.org/content/112/1/244.full OPEN ACCESS

McLean JS* (2014) Advancements toward a systems level understanding of the human oral microbiome. Front Cell Infect Microbiol 4:98. PMCID: PMC4114298 http://journal.frontiersin.org/article/10.3389/fcimb.2014.00098/abstract

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 http://www.nature.com/nrg/journal/v15/n9/full/nrg3785.html

McLean, JS.* and R. Lasken (2014). “Single cell genomics of bacterial pathogens: outlook for infectious disease research.” Genome Medicine 6(11): 108. http://genomemedicine.com/content/6/11/108

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 http://www.microbiomejournal.com/content/1/1/25

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 http://genome.cshlp.org/content/23/5/867.long

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 http://www.pnas.org/content/110/26/E2390.full

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 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032219

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. http://www.nature.com/ismej/journal/v2/n2/full/ismej2007107a.html

Additional publications

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

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

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.

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).

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.

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).

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.

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).

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

Bor B, Poweleit N, Bois JS, Cen L, Bedree JK, Zhou ZH, Gunsalus RP, Lux R, McLean JS, He X, Shi W. 2015. 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#

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

Guo L, McLean JS, Lux R, He X, Shi W. 2015. 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

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 http://www.nature.com/ismej/journal/v8/n3/full/ismej2013172a.html

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

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

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

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

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

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

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.

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.

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.

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

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

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.

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