User:Eoin Brodie

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Contact Info

Eoin Brodie

• Eoin Brodie
• Lawrence Berkeley National Lab
• 1 Cyclotron Rd.
• MS70A-3317
• Berkeley, CA 94720, USA
• Email me through OpenWetWare
• greengenes.lbl.gov
• Official Page

I am a Microbial Ecologist at Lawrence Berkeley National Lab]. Research in our group focuses on determining and better understanding the factors that structure and control microbial communities and the functional implications of alterations in community composition.

For this reason our research involves a wide range of microbial systems including surface and subsurface soils, deep subsurface environments, invertebrate guts, watersheds and contaminated aquifers, urban aerosols and various mammalian microbiomes.

To assess microbial community composition in a high-throughput and high-resolution manner we employ state-of-the-science microarray and DNA sequencing technologies and relate microbiological parameters to functional and physical properties of ecosystems using stable-isotopes, biochemical assays, geochemical/geophysical measurements and statistical modeling.

We learned about OpenWetWare from Colleagues, and have joined to contribute protocols developed in our lab.

Education

• 2001, PhD, Microbial Ecology, University College Dublin, Ireland
• 1996, BS, Microbiology, University College Dublin, Ireland

Research interests

1. Molecular microbial ecology
2. Bioremediation
3. Human microbiome
4. Stable-isotope probing

Publications

1. West KA, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PK, Feil H, Andersen GL, Zinder SH, and Alvarez-Cohen L. Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains. Appl Environ Microbiol. 2008 Jun;74(11):3533-40. DOI:10.1128/AEM.01835-07 |
2. Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, and Alvarez-Cohen L. Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. Appl Environ Microbiol. 2008 May;74(9):2864-72. DOI:10.1128/AEM.02208-07 |
3. Lynch SV, Dixon L, Benoit MR, Brodie EL, Keyhan M, Hu P, Ackerley DF, Andersen GL, and Matin A. Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms. Antimicrob Agents Chemother. 2007 Oct;51(10):3650-8. DOI:10.1128/AAC.00601-07 |
4. Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, and Bristow J. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol. 2007 Jun;45(6):1954-62. DOI:10.1128/JCM.02187-06 |
5. DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, and Andersen GL. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol. 2007 Apr;53(3):371-83. DOI:10.1007/s00248-006-9134-9 |
6. Brodie EL, DeSantis TZ, Parker JP, Zubietta IX, Piceno YM, and Andersen GL. Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):299-304. DOI:10.1073/pnas.0608255104 |
7. Lin LH, Wang PL, Rumble D, Lippmann-Pipke J, Boice E, Pratt LM, Sherwood Lollar B, Brodie EL, Hazen TC, Andersen GL, DeSantis TZ, Moser DP, Kershaw D, and Onstott TC. Long-term sustainability of a high-energy, low-diversity crustal biome. Science. 2006 Oct 20;314(5798):479-82. DOI:10.1126/science.1127376 |
8. Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, and Firestone MK. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol. 2006 Sep;72(9):6288-98. DOI:10.1128/AEM.00246-06 |
9. DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, and Andersen GL. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W394-9. DOI:10.1093/nar/gkl244 |
10. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006 Jul;72(7):5069-72. DOI:10.1128/AEM.03006-05 |
11. Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Chang HW, Watson D, Brodie EL, Hazen TC, and Keller M. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol. 2006 May;72(5):3291-301. DOI:10.1128/AEM.72.5.3291-3301.2006 |
12. Hu P, Brodie EL, Suzuki Y, McAdams HH, and Andersen GL. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol. 2005 Dec;187(24):8437-49. DOI:10.1128/JB.187.24.8437-8449.2005 |
13. Tokunaga TK, Wan J, Pena J, Brodie EL, Firestone MK, Hazen TC, Sutton SR, Lanzirotti A, and Newville M. Uranium reduction in sediments under diffusion-limited transport of organic carbon. Environ Sci Technol. 2005 Sep 15;39(18):7077-83. DOI:10.1021/es050221a |
14. Lynch SV, Brodie EL, and Matin A. Role and regulation of sigma S in general resistance conferred by low-shear simulated microgravity in Escherichia coli. J Bacteriol. 2004 Dec;186(24):8207-12. DOI:10.1128/JB.186.24.8207-8212.2004 |
15. Kennedy N, Brodie E, Connolly J, and Clipson N. Seasonal influences on fungal community structure in unimproved and improved upland grassland soils. Can J Microbiol. 2006 Jul;52(7):689-94. DOI:10.1139/w06-015 |
16. Wan J, Tokunaga TK, Brodie E, Wang Z, Zheng Z, Herman D, Hazen TC, Firestone MK, and Sutton SR. Reoxidation of bioreduced uranium under reducing conditions. Environ Sci Technol. 2005 Aug 15;39(16):6162-9. DOI:10.1021/es048236g |
17. Kennedy N, Brodie E, Connolly J, and Clipson N. Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms. Environ Microbiol. 2004 Oct;6(10):1070-80. DOI:10.1111/j.1462-2920.2004.00638.x |
18. Brodie E, Edwards S, and Clipson N. Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem. Microb Ecol. 2002 Oct;44(3):260-70. DOI:10.1007/s00248-002-2012-1 |

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