Publications

Recent Peer-Reviewed Publications

2024

Bedree, JosephK, Jacob Bourgeois, Pooja Balani, Lujia Cen, Erik Hendrickson, Kristopher Kerns, Andrew Camilli, Jeffrey S McLean, Xuesong He. Identifying essential genes in Schaalia odontolytica using a highly-saturated transposon library bioRxiv 2024.07.17.604004; doi: https://doi.org/10.1101/2024.07.17.604004

Zhong Q, Liao B, Liu J, Shen W, Wang J, Wei L, Ma Y, Dong PT, Bor B, McLean JS, Chang Y, Shi W, Cen L, Wu M, Liu J, Li Y, He X, Le S Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence. Proc Natl Acad Sci U S A. 2024 Apr 16;121(16):e2319790121. doi: 10.1073/pnas.2319790121. Epub 2024 Apr 9. PMID: 38593079

Pu-Ting Dong, Jing Tian, Koseki J Kobayashi-Kirschvink, Lujia Cen, Jeffrey S McLean, Batbileg Bor, Wenyuan Shi, Xuesong He, Episymbiotic Saccharibacteria induce intracellular lipid droplet production in their host bacteria, The ISME Journal, 2024 https://doi.org/10.1093/ismejo/wrad034

Rashidi, A., Gem, H., McLean, J.S., Kerns, K., Dean, D.R., Dey, N. & Minot, S. Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults. https://www.ncbi.nlm.nih.gov/pubmed/38228614 Sci Data 11: 75, 2024

2023

Kerns, K.A., Bamashmous, S., Hendrickson, E.L., Kotsakis, G.A., Leroux, B.G., Daubert, D.D., Roberts, F.A., Chen, D., Trivedi, H.M., Darveau, R.P. & McLean, J.S. Localized microbially induced inflammation influences distant healthy tissues in the human oral cavity. Proceedings of the National Academy of Sciences 120: e2306020120, 2023

Hendrickson, E.L., Bor, B., Kerns, K.A., Cen, L., Shi, W., He, X., McLean J.S. 2023. Ultrasmall epibiont Nanosynbacter lyticus strain TM7x and host bacterial transcriptional activity after initial parasitism. J. Oral Microbiol. DOI: 10.1080/20002297.2023.2287349

Fine, N., Barbour, A., Kaura, K., Kerns, K.A., Chen, D., Trivedi, H.M., Gomez, J., Sabharwal, A., McLean, J.S., Darveau, R.P. & Glogauer, M. Effects of a stabilized stannous fluoride dentifrice on clinical, immunomodulatory, and microbial outcomes in a human experimental gingivitis model. https://www.ncbi.nlm.nih.gov/pubmed/37885337J Periodontol , 2023

Dong, P., Tian, J., Kobayashi-Kirschvink, K. J., Cen, L., McLean, J. S., Bor, B., Shi, W., He, X., (2023) Episymbiotic bacterium induces intracellular lipid droplet production in its host bacteria. bioRxiv. PDF

Baker, J.L., Mark Welch, J.L., Kauffman, K.M., McLean, J.S. & He, X. The oral microbiome: diversity, biogeography and human health. https://doi.org/10.1038/s41579-023-00963-6 Nature Reviews Microbiology, 2023

Access at:  http://rdcu.be/dlW64

Wang, Y., Gallagher, L.A., Andrade, P.A., Liu, A., Humphreys, I.R., Turkarslan, S., Cutler, K.J., Arrieta-Ortiz, M.L., Li, Y., Radey, M.C., McLean, J.S., Cong, Q., Baker, D., Baliga, N.S., Peterson, S.B. & Mougous, J.D. Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle. https://doi.org/10.1016/j.cell.2023.08.017 Cell, Online Sept 7 2023

Bedree JK, Kerns K, Chen T, Lima BP, Liu G, Ha P, Shi J, Pan HC, Kim JK, Tran L, Minot SS, Hendrickson EL, Lamont EI, Schulte F, Hardt M, Stephens D, Patel M, Kokaras A, Stodieck L, Shirazi-Fard Y, Wu B, Kwak JH, Ting K, Soo C, McLean JS, He X, Shi W. Specific host metabolite and gut microbiome alterations are associated with bone loss during spaceflight. Cell Rep. 2023 Apr 10:112299. doi: 10.1016/j.celrep.2023.112299. Epub ahead of print. PMID: 37080202.

Rashidi, A., Koyama, M., Dey, N., McLean, J.S., Hill, G.R. (2023). Colonization Resistance is Dispensable for Segregation of Oral and Gut Microbiota. BMC Med Genomics Vol. 16, No. 31. https://doi.org/10.1186/s12920-023-01449-3

2022

Liu, J., Utter, D.R., Nie, J., Kerns, K.A., Lamont, E.I., Hendrickson, E.L., Wang, X., McLean, J.S., He, X., Bor, B. (2022). Draft Genome Sequences of Nine “Candidatus Nanosynbacter sp. HMT-352” Strains Cultured from the Human Oral Cavity. Microbiology Resource Announcments: Vol. 11, No. 8. https://doi.org/10.1128/mra.00403-22

Cen, L., Chang, Y., Bedree, J.K., Ma, Y., Zhong, Q., Utter, D.R., Dong, P., Lux, R., Bor, B., Liu, J., McLean, J.S., Le, S., He, X. (2022). Exploitation of a Bacterium -Encoded Lytic Transglycosylase by a Human Oral Lytic Phage to Facilitate Infection. Journal of Virology: Vol 96, No. 17. https://doi.org/10.1128/jvi.01063-22

Hendrickson, E.L., Bor, B., Kerns, K.A., Lamont, E.I., Chang, Y., Liu, J., Cen, L., Schulte, F., Hardt, M., Shi, W., He, X., McLean, J.S. (2022). Transcriptome of Epibiont Saccharibacteria Nanosynbacter lyticus Strain TM7x During Establishment of Symbiosis. Journal of Bacteriology: Vol 204, No. 9. https://doi.org/10.1128/jb.00112-22

Nie, J., Utter, D.R., Kerns, K.A., Lamont, E.I., Hendrickson, E.L., Liu, J., Wu, T., He, X., McLean, J.S. & Bor, B. (2022). Strain-Level Variation and Diverse Host Bacterial Responses in Episymbiotic Saccharibacteria. mSystems: e0148821. https://doi.org/10.1128/msystems.01488-21

Tian, J., Utter, D.R., Cen, L., Dong, P., Shi, W., Bor. B., Qin, M., McLean, J.S., & He, X. (2022). Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment. Proceedings of the National Academy of Sciences of the United States of America, 119(2), e2114909119. https://doi.org/10.1073/pnas.2114909119

2021

Bamashmous, S., Kotsakis, G. A., Kerns, K. A., Leroux, B. G., Zenobia, C., Chen, D., Trivedi, H. M., McLean, J. S*., & Darveau, R. P. (2021). Human variation in gingival inflammation. Proceedings of the National Academy of Sciences of the United States of America, 118(27), e2012578118. https://doi.org/10.1073/pnas.2012578118

• Raw read and sample meta data are available on NCBI SRA, https://www.ncbi.nlm.nih.gov/sra (BioProject PRJNA615201) Data workflows and R code publicly available on GitHub (https://github.com/mcleanlab/HVGI_Study) and contains all necessary raw and processed files, (i.e., .biom, metadata.txt, .tree).

• This Week in Microbiology (TWIM) Episode 254: Episymbionts Are Good For You. https://asm.org/Podcasts/TWiM/Episodes/Episymbionts-Are-Good-For-You-TWiM-254

2020

Lamont, E.I., Gadkari, A., Kerns, K.A., To, T.T., Daubert, D., Kotsakis, G., Bor, B., He, X., McLean, J.S.* Modified SHI medium supports growth of a disease-state subgingival polymicrobial community in vitro. Molecular Oral Microbiology. 2020 Nov 11. https://doi.org/10.1111/omi.12323 PubMed PMID: 33174294

• TM7_G3_3_HMT_351_EL001 assembly accessible at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA663916

Utter, D.R., He, X., Cavanaugh, C.M., McLean, J.S., Bor., B. The saccharibacterium TM7x elicits differential responses across its hosts range. ISME 2020 Aug 24. https://doi.org/10.1038/s41396-020-00736-6

Lamont, E.I., Hendrickson, E.L., McLean, J.S., He, X., Bor, B. Complete Genome Sequence of Strain BB001, a Novel Epibiont Bacterium from the Candidate Phylum Saccharibacteria (TM7) ASM. 2020 Aug 20.  https://doi.org/10.1128/MRA.00810-20 PubMed PMID: 32816985

McLean, J.S.*, Bor, B., Kerns, K.A., Liu, Q., To, T.T., Solden, L., Hendrickson, E.L., Wrighton, K., Shi, W., and He, X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Reports 32. 2020 July 21. https://doi.org/10.1016/j.celrep.2020.107939 PubMed PMID: 32698001

• Genomes G5, G3, G6, G1: Bioproject PRJNA38479 https://www.ncbi.nlm.nih.gov/bioproject/384792

• Our work on nano-sized parasitic bacteria covered in TWiM episode 222

• https://asm.org/Podcasts/TWiM/Episodes/Biosensors-in-bacteria-TWiM-222

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 19.   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 DOI: 10.7554/eLife.54318 

• BioProject Accession No: PRJEB35672

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. GEO Accession No : GSE122289

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 Immun. 2019 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. Genome Accession No : PRJNA525688 Metagenome/Transcriptome Accession No : PRJNA525517

Sriharsha Grevich, Peggy Lee, Jeffrey McLean, Brian Leroux, Sarah Ringold, Kyle Hager, Mitchell Brittnacher, Hillary Hayden, Samuel Miller, Anne Stevens. Oral Microbial Profile in Juvenile Idiopathic Arthritis ARTHRITIS & RHEUMATOLOGY 69, 213-214

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

McLean, J.S., Bor, B., To, T.T., Liu, Q., Kerns, K.A., Solden, L., Wrighton, K., He, X. & Shi, W. Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria. https://www.biorxiv.org/content/biorxiv/early/2018/02/02/258137.full.pdf bioRxiv, 2018,

McLean, J.S.* , Bor, B., To, T.T., Liu, Q., Kerns, K.A., Solden, L.M., Wrighton, K.C., He, X. & Shi, W. Independent Acquisition and Adaptation of Ultra-Small Bacteria with Reduced Genomes from the Phylum Saccharibacteria to Human Hosts. available as a preprint while under review at Cell (https://ssrn.com/abstract=3192029) BioProject Accession No : PRJNA384792

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 BioProject Accession No : PRJNA398963

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

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. Front. Microbiol. | doi: 10.3389/fmicb.2018.02049

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. GEO Accession No : GSE110275

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. BioProject Accession No : PRJNA289925

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). GenBank Accession No : LLVT00000000 and MG941013

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

2017

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 GenBank Accession No : LOEL00000000

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.

Hanson-Drury S, To TT, Liu Q, Vo AT, Kim M, Watling M, Bumgarner RS, McLean JS. Draft Genome Sequence of Tannerella forsythia Clinical Isolate 9610. Genome Announc. 2017 Mar 23;5(12):e00024-17. doi: 10.1128/genomeA.00024-17. PMID: 28336586; PMCID: PMC5364211

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).

2016

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). GenBank Accession No : LLVT00000000

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.

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). BioProject Accession No : PRJNA292354

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

To TT, Liu Q, Watling M, Darveau RP, Bumgarner RE, McLean JS*. (2016) Genome sequence of low-passage clinical isolate Porphyromonas gingivalis MP4-504. Genome Announcements In press. GenBank Accession No : LOEL00000000

Edlund A, Q Liu, M Watling, TT To, RE Bumgarner, X He, W Shi, JS McLean* (2016) . High-quality draft genome sequence of low-pH-active Veillonella parvula strain SHI-1, isolated from human saliva within an in vitro oral biofilm model Genome Announcements 4 (1), e01684-15. GenBank Accession No : LOJO00000000

2015

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. 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. (2015)  International Society for Microbial Ecology Journal (ISME) http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201572a.html OPEN ACCESS.

BioProject Accession No : PRJNA264728

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. BioProject Accession No : PRJNA241438

McLean, J. S.*, Q. Liu, J. Thompson, A. Edlund and S. Kelley (2015). "Draft Genome Sequence of "Candidatus Bacteroides periocalifornicus," a New Member of the Bacteriodetes Phylum Found within the Oral Microbiome of Periodontitis Patients." Genome Announc 3(6). GenBank Accession No : LIIK00000000

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. http://link.springer.com/article/10.1007%2Fs00248-015-0711-7#. GenBank Accession No : CP007496

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

2014

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. BioProject Accession No : PRJNA28331

2013

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.150433.112.

PMCID: PMC3638142 http://genome.cshlp.org/content/23/5/867.long BioProject Accession No : PRJNA167667

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 BioProject Accession No : PRJNA193445 GenBank Accession No : KF057992

Nurk, S., Bankevich, A., Antipov, D., Gurevich, A.A., Korobeynikov, A., Lapidus, A., Prjibelski, A.D., Pyshkin, A., Sirotkin, A., Sirotkin, Y., Stepanauskas, R., Clingenpeel, S.R., Woyke, T., McLean, J.S., Lasken, R., Tesler, G., Alekseyev, M.A. & Pevzner, P.A. (2013) Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products. Journal of computational biology : a journal of computational molecular cell biology 20, 714-737

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

Zeigler Allen, L., Ishoey, T., Novotny, M. A., McLean, J. S., Lasken, R. S., and Williamson, S. J., 2013, Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics': J Vis Exp, no. 75, p. e3899

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

2012

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

Ahmed, B., B. Cao, J. S. McLean, T. Ica, A. Dohnalkova, O. Istanbullu, A. Paksoy, J. K. Fredrickson and H. Beyenal (2012). "Fe(III) Reduction and U(VI) Immobilization by Paenibacillus sp. 300A Isolated from Hanford 300A Subsurface Sediments." Appl Environ Microbiol.; published ahead of print 7 September 2012, doi:10.1128/AEM.01844-12

2000-2011

• 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

• Renslow, R. S.; Majors, P. D.; McLean, J. S.; Fredrickson, J. K.; Ahmed, B.; Beyenal, H., (2010) In situ effective diffusion coefficient profiles in live biofilms using pulsed-field gradient nuclear magnetic resonance. Biotechnol Bioeng, 106 (6), 928-37

• 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

• Reardon, C.L., Dohnalkova, A.C., Nachimuthu, P., Kennedy, D.W., Saffarini, D.A., Arey, B.W., Shi, L., Wang, Z., Moore, D., McLean, J.S., et al. 2009. Role of outer-membrane cytochromes MtrC and OmcA in the biomineralization of ferrihydrite by Shewanella oneidensis MR-1. Geobiology. PMID:20002197

• 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

• 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

• Majors, P. D., J. S. McLean, and J. C. M. Scholten. (2008) NMR bioreactor development for live in-situ microbial functional analysis. Journal of Magnetic Resonance. 2008 May;192(1):159-66.

• Gorby, Y.A., J.S. McLean,  A. Korenevsky, , K. Rosso, M. El-Naggar, and T. J. Beveridge. 2008. Redox-Reactive Membrane Vesicles produced by Shewanella. Geobiology. Jun;6(3):232-41.

• 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.

• Elias, D. A., S. L. Tollaksen, D. W. Kennedy, H. M. Mottaz, C. S. Giometti, J. S. McLean, E. A. Hill, G. E. Pinchuk, M. S. Lipton, J. K. Fredrickson, and Y. A. Gorby. (2007). The influence of cultivation methods on Shewanella oneidensis physiology and proteome expression. Arch Microbiol. 189(4):313-2.

• Biju VP, D Pan, YA Gorby, JK Fredrickson,JS Mclean, D Saffarini, and HP Lu. (2007). "Combined Spectroscopic and Topographic Characterization of Nanoscale Domains and Their Distributions of a Redox Protein on Bacterial Cell Surfaces Under Electron-Acceptor Limited and Excessed Conditions."  Journal of the American Chemical Society 23(3):1333-1338.

• 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.

• Marshall MJ, AS Beliaev,  A Dohnalkova, DW Kennedy, L Shi, Z Wang, MI Boyanov, B Lai, KM  Kemner, JS McLean, SB Reed, DE Culley, VL Bailey, CJ Simonson, D Saffarini, MF Romine, JM Zachara, and JK Fredrickson.  (2006).  "c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis."  PloS Biology 4(8):1324-1333. 

• Good MS, CF Wend, LJ Bond, JS Mclean, PD Panetta, S Ahmed, SL Crawford, and DS Daly.  (2006).  "An Estimate of Biofilm Properties using an Acoustic Microscope."  IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 53(9):1637-1648.

• Harvey SD, GM Mong, RM Ozanich, JS McLean, SM Goodwin, NB Valentine, and JK Fredrickson.  (2006).  "Preparation and evaluation of spore-specific affinity- augmented bio-imprinted beads."  Analytical and Bioanalytical Chemistry 386(2):211-219.  doi:10.1007/s00216-006-0622-z

• Majors PD, JS McLean, JK Fredrickson, and RA Wind. (2005). “NMR methods for in-situ biofilm metabolism studies: spatial and temporal resolved measurements.” Water Science & Technology 52(7): 7–12

• Majors, PD, JS McLean, GE Pinchuk, JK Fredrickson, YA Gorby, KR Minard RA Wind. (2005). "NMR methods for in-situ biofilm metabolism studies." Journal of Microbiological Methods 62(3): 377-344.

• Wunschel, DS, EA Hill, JS McLean, K Jarman, YA Gorby, and N. Valentine. (2005). Effects of varied pH, growth rate and temperature using controlled fermentation and batch culture on Matrix Assisted Laser Desorption/Ionization whole cell protein fingerprints. Journal of Microbiological Methods. Sep;62(3):259-71.

• Hu JZ, RA Wind, JS McLean, YA Gorby, CT Resch, and JK Fredrickson (2004). High Resolution 1H NMR Spectroscopy of Metabolically Active Microorganisms Using Non-Destructive Magic Angle Spinning. Spectroscopy. December, Volume 19, Number 12

• 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.