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Items: 1 to 50 of 103

1.

Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants.

Wood LF, Brown BP, Lennard K, Karaoz U, Havyarimana E, Passmore JS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie EL, Sodora DL, Jaspan HB.

Clin Infect Dis. 2018 Sep 28;67(8):1237-1246. doi: 10.1093/cid/ciy265.

2.

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly.

Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Karaoz U, Loqué D, Bowen BP, Firestone MK, Northen TR, Brodie EL.

Nat Microbiol. 2018 Apr;3(4):470-480. doi: 10.1038/s41564-018-0129-3. Epub 2018 Mar 19.

PMID:
29556109
3.

Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity.

Karaoz U, Couradeau E, da Rocha UN, Lim HC, Northen T, Garcia-Pichel F, Brodie EL.

MBio. 2018 Mar 6;9(2). pii: e01366-16. doi: 10.1128/mBio.01366-16.

4.

Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate.

D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J.

Stand Genomic Sci. 2017 Nov 15;12:67. doi: 10.1186/s40793-017-0279-6. eCollection 2017.

5.

Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits.

Chase AB, Karaoz U, Brodie EL, Gomez-Lunar Z, Martiny AC, Martiny JBH.

MBio. 2017 Nov 14;8(6). pii: e01809-17. doi: 10.1128/mBio.01809-17.

6.

Probabilistic Invasion Underlies Natural Gut Microbiome Stability.

Obadia B, Güvener ZT, Zhang V, Ceja-Navarro JA, Brodie EL, Ja WW, Ludington WB.

Curr Biol. 2017 Jul 10;27(13):1999-2006.e8. doi: 10.1016/j.cub.2017.05.034. Epub 2017 Jun 15.

7.

Reoxidation of Chromium(III) Products Formed under Different Biogeochemical Regimes.

Varadharajan C, Beller HR, Bill M, Brodie EL, Conrad ME, Han R, Irwin C, Larsen JT, Lim HC, Molins S, Steefel CI, van Hise A, Yang L, Nico PS.

Environ Sci Technol. 2017 May 2;51(9):4918-4927. doi: 10.1021/acs.est.6b06044. Epub 2017 Apr 18.

8.

Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.

Yabusaki SB, Wilkins MJ, Fang Y, Williams KH, Arora B, Bargar J, Beller HR, Bouskill NJ, Brodie EL, Christensen JN, Conrad ME, Danczak RE, King E, Soltanian MR, Spycher NF, Steefel CI, Tokunaga TK, Versteeg R, Waichler SR, Wainwright HM.

Environ Sci Technol. 2017 Mar 21;51(6):3307-3317. doi: 10.1021/acs.est.6b04873. Epub 2017 Mar 7.

9.

Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer.

Jewell TN, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, Beller HR.

Front Microbiol. 2017 Jan 25;8:40. doi: 10.3389/fmicb.2017.00040. eCollection 2017.

10.

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis).

Ben Guerrero E, Soria M, Salvador R, Ceja-Navarro JA, Campos E, Brodie EL, Talia P.

Front Microbiol. 2016 Dec 27;7:2093. doi: 10.3389/fmicb.2016.02093. eCollection 2016.

11.

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF.

Nat Commun. 2016 Oct 24;7:13219. doi: 10.1038/ncomms13219.

12.

Microbial legacies alter decomposition in response to simulated global change.

Martiny JB, Martiny AC, Weihe C, Lu Y, Berlemont R, Brodie EL, Goulden ML, Treseder KK, Allison SD.

ISME J. 2017 Feb;11(2):490-499. doi: 10.1038/ismej.2016.122. Epub 2016 Oct 14.

13.

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass.

Nuccio EE, Anderson-Furgeson J, Estera KY, Pett-Ridge J, De Valpine P, Brodie EL, Firestone MK.

Ecology. 2016 May;97(5):1307-18.

14.

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL.

MBio. 2016 May 13;7(3). pii: e00714-16. doi: 10.1128/mBio.00714-16.

15.

Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism.

Bouskill NJ, Wood TE, Baran R, Ye Z, Bowen BP, Lim H, Zhou J, Nostrand JD, Nico P, Northen TR, Silver WL, Brodie EL.

Front Microbiol. 2016 Apr 20;7:525. doi: 10.3389/fmicb.2016.00525. eCollection 2016.

16.

Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition.

Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL.

Front Microbiol. 2016 Mar 15;7:323. doi: 10.3389/fmicb.2016.00323. eCollection 2016.

17.

Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer.

Jewell TN, Karaoz U, Brodie EL, Williams KH, Beller HR.

ISME J. 2016 Sep;10(9):2106-17. doi: 10.1038/ismej.2016.25. Epub 2016 Mar 4.

18.

MICROBIOME. A unified initiative to harness Earth's microbiomes.

Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA; Unified Microbiome Initiative Consortium.

Science. 2015 Oct 30;350(6260):507-8. doi: 10.1126/science.aac8480. Epub 2015 Oct 28. No abstract available.

19.

Exometabolite niche partitioning among sympatric soil bacteria.

Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Da Rocha UN, Chakraborty R, Bowen BP, Karaoz U, Cadillo-Quiroz H, Garcia-Pichel F, Northen TR.

Nat Commun. 2015 Sep 22;6:8289. doi: 10.1038/ncomms9289.

20.

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons.

Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M.

MBio. 2015 Aug 4;6(4):e00746. doi: 10.1128/mBio.00746-15.

21.

Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampei.

Vega FE, Brown SM, Chen H, Shen E, Nair MB, Ceja-Navarro JA, Brodie EL, Infante F, Dowd PF, Pain A.

Sci Rep. 2015 Jul 31;5:12525. doi: 10.1038/srep12525.

22.

Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee.

Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, Kosina P, Infante F, Northen TR, Brodie EL.

Nat Commun. 2015 Jul 14;6:7618. doi: 10.1038/ncomms8618.

23.

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.

Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL.

Front Microbiol. 2015 Apr 14;6:277. doi: 10.3389/fmicb.2015.00277. eCollection 2015.

24.

Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens.

Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV.

PLoS One. 2015 Feb 6;10(2):e0117617. doi: 10.1371/journal.pone.0117617. eCollection 2015.

25.

Cellulolytic potential under environmental changes in microbial communities from grassland litter.

Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JB, Martiny AC.

Front Microbiol. 2014 Nov 25;5:639. doi: 10.3389/fmicb.2014.00639. eCollection 2014.

26.

Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products.

Beller HR, Yang L, Varadharajan C, Han R, Lim HC, Karaoz U, Molins S, Marcus MA, Brodie EL, Steefel CI, Nico PS.

Environ Sci Technol. 2014 Sep 16;48(18):10699-706. doi: 10.1021/es5016982. Epub 2014 Aug 13.

PMID:
25084058
27.

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.

Closek CJ, Sunagawa S, DeSalvo MK, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M.

ISME J. 2014 Dec;8(12):2411-22. doi: 10.1038/ismej.2014.85. Epub 2014 Jun 20.

28.

Interactions between Bacillus anthracis and plants may promote anthrax transmission.

Ganz HH, Turner WC, Brodie EL, Kusters M, Shi Y, Sibanda H, Torok T, Getz WM.

PLoS Negl Trop Dis. 2014 Jun 5;8(6):e2903. doi: 10.1371/journal.pntd.0002903. eCollection 2014 Jun.

29.

Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes.

Wells GF, Wu CH, Piceno YM, Eggleston B, Brodie EL, Desantis TZ, Andersen GL, Hazen TC, Francis CA, Criddle CS.

Appl Microbiol Biotechnol. 2014 May;98(10):4723-36. doi: 10.1007/s00253-014-5564-3. Epub 2014 Feb 20.

PMID:
24553968
30.

Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.

Ma Y, Madupu R, Karaoz U, Nossa CW, Yang L, Yooseph S, Yachimski PS, Brodie EL, Nelson KE, Pei Z.

J Virol. 2014 May;88(9):4786-97. doi: 10.1128/JVI.00093-14. Epub 2014 Feb 12.

31.

Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China.

Briggs BR, Brodie EL, Tom LM, Dong H, Jiang H, Huang Q, Wang S, Hou W, Wu G, Huang L, Hedlund BP, Zhang C, Dijkstra P, Hungate BA.

Environ Microbiol. 2014 Jun;16(6):1579-91. doi: 10.1111/1462-2920.12311. Epub 2013 Nov 14.

PMID:
24148100
32.

Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries.

Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JB, Martiny AC, Brodie EL.

Front Microbiol. 2013 Sep 23;4:282. doi: 10.3389/fmicb.2013.00282. eCollection 2013.

33.

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus.

Ceja-Navarro JA, Nguyen NH, Karaoz U, Gross SR, Herman DJ, Andersen GL, Bruns TD, Pett-Ridge J, Blackwell M, Brodie EL.

ISME J. 2014 Jan;8(1):6-18. doi: 10.1038/ismej.2013.134. Epub 2013 Aug 29.

34.

Export of submicron particulate organic matter to mesopelagic depth in an oligotrophic gyre.

Close HG, Shah SR, Ingalls AE, Diefendorf AF, Brodie EL, Hansman RL, Freeman KH, Aluwihare LI, Pearson A.

Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):12565-70. doi: 10.1073/pnas.1217514110. Epub 2013 Jul 15.

35.

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust.

Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A.

ISME J. 2013 Nov;7(11):2178-91. doi: 10.1038/ismej.2013.83. Epub 2013 Jun 6.

36.

Biogeography of bacterioplankton in the tropical seawaters of Singapore.

Lau SC, Zhang R, Brodie EL, Piceno YM, Andersen G, Liu WT.

FEMS Microbiol Ecol. 2013 May;84(2):259-69. doi: 10.1111/1574-6941.12057. Epub 2013 Jan 15.

37.

Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought.

Bouskill NJ, Lim HC, Borglin S, Salve R, Wood TE, Silver WL, Brodie EL.

ISME J. 2013 Feb;7(2):384-94. doi: 10.1038/ismej.2012.113. Epub 2012 Nov 15.

38.

Trait-based representation of biological nitrification: model development, testing, and predicted community composition.

Bouskill NJ, Tang J, Riley WJ, Brodie EL.

Front Microbiol. 2012 Oct 18;3:364. doi: 10.3389/fmicb.2012.00364. eCollection 2012.

39.

Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1.

Beller HR, Han R, Karaoz U, Lim H, Brodie EL.

Appl Environ Microbiol. 2013 Jan;79(1):63-73. doi: 10.1128/AEM.02496-12. Epub 2012 Oct 12.

40.

Cystic fibrosis transmembrane conductance regulator knockout mice exhibit aberrant gastrointestinal microbiota.

Lynch SV, Goldfarb KC, Wild YK, Kong W, De Lisle RC, Brodie EL.

Gut Microbes. 2013 Jan-Feb;4(1):41-7. doi: 10.4161/gmic.22430. Epub 2012 Oct 12.

41.

Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil.

Hayden HL, Mele PM, Bougoure DS, Allan CY, Norng S, Piceno YM, Brodie EL, Desantis TZ, Andersen GL, Williams AL, Hovenden MJ.

Environ Microbiol. 2012 Dec;14(12):3081-96. doi: 10.1111/j.1462-2920.2012.02855.x. Epub 2012 Oct 8.

PMID:
23039205
42.

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups.

Placella SA, Brodie EL, Firestone MK.

Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10931-6. doi: 10.1073/pnas.1204306109. Epub 2012 Jun 19.

43.

Influence of geogenic factors on microbial communities in metallogenic Australian soils.

Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL, Lu Z, He Z, Zhou J, Wakelin SA.

ISME J. 2012 Nov;6(11):2107-18. doi: 10.1038/ismej.2012.48. Epub 2012 Jun 7.

44.

Metagenomic analysis of a stable trichloroethene-degrading microbial community.

Brisson VL, West KA, Lee PK, Tringe SG, Brodie EL, Alvarez-Cohen L.

ISME J. 2012 Sep;6(9):1702-14. doi: 10.1038/ismej.2012.15. Epub 2012 Mar 1.

45.

Differences in crop bacterial community structure between hoatzins from different geographical locations.

Godoy-Vitorino F, Leal SJ, Díaz WA, Rosales J, Goldfarb KC, García-Amado MA, Michelangeli F, Brodie EL, Domínguez-Bello MG.

Res Microbiol. 2012 Apr;163(3):211-20. doi: 10.1016/j.resmic.2012.01.001. Epub 2012 Jan 21.

PMID:
22313738
46.

High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use.

Mayali X, Weber PK, Brodie EL, Mabery S, Hoeprich PD, Pett-Ridge J.

ISME J. 2012 Jun;6(6):1210-21. doi: 10.1038/ismej.2011.175. Epub 2011 Dec 8.

47.

Soil bacterial communities of a calcium-supplemented and a reference watershed at the Hubbard Brook Experimental Forest (HBEF), New Hampshire, USA.

Sridevi G, Minocha R, Turlapati SA, Goldfarb KC, Brodie EL, Tisa LS, Minocha SC.

FEMS Microbiol Ecol. 2012 Mar;79(3):728-40. doi: 10.1111/j.1574-6941.2011.01258.x. Epub 2011 Dec 15.

48.

Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia.

Wakelin SA, Anand RR, Reith F, Gregg AL, Noble RR, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL.

FEMS Microbiol Ecol. 2012 Feb;79(2):298-311. doi: 10.1111/j.1574-6941.2011.01215.x. Epub 2011 Oct 24.

49.

Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site.

Lee PK, Warnecke F, Brodie EL, Macbeth TW, Conrad ME, Andersen GL, Alvarez-Cohen L.

Environ Sci Technol. 2012 Jan 17;46(2):1044-54. doi: 10.1021/es203005k. Epub 2011 Dec 27.

50.

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows.

Godoy-Vitorino F, Goldfarb KC, Karaoz U, Leal S, Garcia-Amado MA, Hugenholtz P, Tringe SG, Brodie EL, Dominguez-Bello MG.

ISME J. 2012 Mar;6(3):531-41. doi: 10.1038/ismej.2011.131. Epub 2011 Sep 22.

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