Rachel Dutton

Title(s)	Professor, Molecular Biology
School	Vc-academic Affairs
Address	9500 Gilman Drive # La Jolla CA 92093
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Research

Research Activities and Funding

Molecular mechanisms that shape microbial communities
NIH DP2AT010401Sep 30, 2018 - Jun 30, 2023
Role: Principal Investigator

Bibliographic

Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities. mSystems. 2023 Jan 09; e0070122. Saak CC, Pierce EC, Dinh CB, Portik D, Hall R, Ashby M, Dutton RJ. PMID: 36622155.

View in: PubMed Mentions: Translation:Humans Cells
Higher-order interactions shape microbial interactions as microbial community complexity increases. Sci Rep. 2022 12 31; 12(1):22640. Morin MA, Morrison AJ, Harms MJ, Dutton RJ. PMID: 36587027; PMCID: PMC9805437.

View in: PubMed Mentions: Fields:
Sci Science
Translation:Cells
Enhancing untargeted metabolomics using metadata-based source annotation. Nat Biotechnol. 2022 12; 40(12):1774-1779. Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC. PMID: 35798960.

View in: PubMed Mentions: 4 Fields:
Bio Biotechnology
Translation:Humans
Native mass spectrometry-based metabolomics identifies metal-binding compounds. Nat Chem. 2022 01; 14(1):100-109. Aron AT, Petras D, Schmid R, Gauglitz JM, B?ttel I, Antelo L, Zhi H, Nuccio SP, Saak CC, Malarney KP, Thines E, Dutton RJ, Aluwihare LI, Raffatellu M, Dorrestein PC. PMID: 34795435; PMCID: PMC8959065.

View in: PubMed Mentions: 4 Fields:
Che Chemistry
Translation:Cells
Putting microbial interactions back into community contexts. Curr Opin Microbiol. 2022 02; 65:56-63. Pierce EC, Dutton RJ. PMID: 34739927.

View in: PubMed Mentions: 6 Fields:
Mic Microbiology
Translation:Cells
A community resource for paired genomic and metabolomic data mining. Nat Chem Biol. 2021 04; 17(4):363-368. Schorn MA, Verhoeven S, Ridder L, Huber F, Acharya DD, Aksenov AA, Aleti G, Moghaddam JA, Aron AT, Aziz S, Bauermeister A, Bauman KD, Baunach M, Beemelmanns C, Beman JM, Berlanga-Clavero MV, Blacutt AA, Bode HB, Boullie A, Brejnrod A, Bugni TS, Calteau A, Cao L, Carri?n VJ, Castelo-Branco R, Chanana S, Chase AB, Chevrette MG, Costa-Lotufo LV, Crawford JM, Currie CR, Cuypers B, Dang T, de Rond T, Demko AM, Dittmann E, Du C, Drozd C, Dujardin JC, Dutton RJ, Edlund A, Fewer DP, Garg N, Gauglitz JM, Gentry EC, Gerwick L, Glukhov E, Gross H, Gugger M, Guill?n Matus DG, Helfrich EJN, Hempel BF, Hur JS, Iorio M, Jensen PR, Kang KB, Kaysser L, Kelleher NL, Kim CS, Kim KH, Koester I, K?nig GM, Leao T, Lee SR, Lee YY, Li X, Little JC, Maloney KN, M?nnle D, Martin H C, McAvoy AC, Metcalf WW, Mohimani H, Molina-Santiago C, Moore BS, Mullowney MW, Muskat M, Nothias LF, O'Neill EC, Parkinson EI, Petras D, Piel J, Pierce EC, Pires K, Reher R, Romero D, Roper MC, Rust M, Saad H, Saenz C, Sanchez LM, S?rensen SJ, Sosio M, S?ssmuth RD, Sweeney D, Tahlan K, Thomson RJ, Tobias NJ, Trindade-Silva AE, van Wezel GP, Wang M, Weldon KC, Zhang F, Ziemert N, Duncan KR, Cr?semann M, Rogers S, Dorrestein PC, Medema MH, van der Hooft JJJ. PMID: 33589842; PMCID: PMC7987574.

View in: PubMed Mentions: 34 Fields:
Bio Biology Che Chemistry
Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. Nat Microbiol. 2021 01; 6(1):87-102. Pierce EC, Morin M, Little JC, Liu RB, Tannous J, Keller NP, Pogliano K, Wolfe BE, Sanchez LM, Dutton RJ. PMID: 33139882; PMCID: PMC8515420.

View in: PubMed Mentions: 18 Fields:
Mic Microbiology Par Parasitology Vir Virology
Translation:Animals Cells
Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev. 2020 09 01; 44(5):606-630. Saak CC, Dinh CB, Dutton RJ. PMID: 32672812; PMCID: PMC7476777.

View in: PubMed Mentions: 8 Fields:
Mic Microbiology
Translation:Cells PHPublic Health
BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples. J Am Soc Mass Spectrom. 2019 Aug; 30(8):1426-1434. Cleary JL, Luu GT, Pierce EC, Dutton RJ, Sanchez LM. PMID: 30993641; PMCID: PMC6675636.

View in: PubMed Mentions: 6 Fields:
Che Chemistry Techniques
Translation:Animals Cells
Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi. Nat Microbiol. 2019 02; 4(2):244-250. Peters JM, Koo BM, Patino R, Heussler GE, Hearne CC, Qu J, Inclan YF, Hawkins JS, Lu CHS, Silvis MR, Harden MM, Osadnik H, Peters JE, Engel JN, Dutton RJ, Grossman AD, Gross CA, Rosenberg OS. PMID: 30617347; PMCID: PMC6424567.

View in: PubMed Mentions: 53 Fields:
Mic Microbiology Par Parasitology Vir Virology
Translation:Cells
Changes in the genetic requirements for microbial interactions with increasing community complexity. Elife. 2018 09 13; 7. Morin M, Pierce EC, Dutton RJ. PMID: 30211673; PMCID: PMC6175579.

View in: PubMed Mentions: 22 Fields:
Bio Biology
Translation:Cells
Extensive horizontal gene transfer in cheese-associated bacteria. Elife. 2017 06 23; 6. Bonham KS, Wolfe BE, Dutton RJ. PMID: 28644126; PMCID: PMC5526665.

View in: PubMed Mentions: 32 Fields:
Bio Biology
Translation:Cells
Erratum for Kastman et al., "Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species". mBio. 2017 03 21; 8(2). Kastman EK, Kamelamela N, Norville JW, Cosetta CM, Dutton RJ, Wolfe BE. PMID: 28325768; PMCID: PMC5362037.

View in: PubMed Mentions: 1 Fields:
Mic Microbiology
mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. mSystems. 2016 Sep-Oct; 1(5). Bokulich NA, Rideout JR, Mercurio WG, Shiffer A, Wolfe B, Maurice CF, Dutton RJ, Turnbaugh PJ, Knight R, Caporaso JG. PMID: 27822553; PMCID: PMC5080401.

View in: PubMed Mentions: 37
Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species. mBio. 2016 10 18; 7(5). Kastman EK, Kamelamela N, Norville JW, Cosetta CM, Dutton RJ, Wolfe BE. PMID: 27795388; PMCID: PMC5082897.

View in: PubMed Mentions: 39 Fields:
Mic Microbiology
Translation:Animals Cells PHPublic Health
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016 08 09; 34(8):828-837. Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen DD, Watrous J, Kapono CA, Luzzatto-Knaan T, Porto C, Bouslimani A, Melnik AV, Meehan MJ, Liu WT, Cr?semann M, Boudreau PD, Esquenazi E, Sandoval-Calder?n M, Kersten RD, Pace LA, Quinn RA, Duncan KR, Hsu CC, Floros DJ, Gavilan RG, Kleigrewe K, Northen T, Dutton RJ, Parrot D, Carlson EE, Aigle B, Michelsen CF, Jelsbak L, Sohlenkamp C, Pevzner P, Edlund A, McLean J, Piel J, Murphy BT, Gerwick L, Liaw CC, Yang YL, Humpf HU, Maansson M, Keyzers RA, Sims AC, Johnson AR, Sidebottom AM, Sedio BE, Klitgaard A, Larson CB, P CAB, Torres-Mendoza D, Gonzalez DJ, Silva DB, Marques LM, Demarque DP, Pociute E, O'Neill EC, Briand E, Helfrich EJN, Granatosky EA, Glukhov E, Ryffel F, Houson H, Mohimani H, Kharbush JJ, Zeng Y, Vorholt JA, Kurita KL, Charusanti P, McPhail KL, Nielsen KF, Vuong L, Elfeki M, Traxler MF, Engene N, Koyama N, Vining OB, Baric R, Silva RR, Mascuch SJ, Tomasi S, Jenkins S, Macherla V, Hoffman T, Agarwal V, Williams PG, Dai J, Neupane R, Gurr J, Rodr?guez AMC, Lamsa A, Zhang C, Dorrestein K, Duggan BM, Almaliti J, Allard PM, Phapale P, Nothias LF, Alexandrov T, Litaudon M, Wolfender JL, Kyle JE, Metz TO, Peryea T, Nguyen DT, VanLeer D, Shinn P, Jadhav A, M?ller R, Waters KM, Shi W, Liu X, Zhang L, Knight R, Jensen PR, Palsson BO, Pogliano K, Linington RG, Guti?rrez M, Lopes NP, Gerwick WH, Moore BS, Dorrestein PC, Bandeira N. PMID: 27504778; PMCID: PMC5321674.

View in: PubMed Mentions: 1063 Fields:
Bio Biotechnology
From Sample to Multi-Omics Conclusions in under 48 Hours. mSystems. 2016 Mar-Apr; 1(2). Quinn RA, Navas-Molina JA, Hyde ER, Song SJ, Vázquez-Baeza Y, Humphrey G, Gaffney J, Minich JJ, Melnik AV, Herschend J, DeReus J, Durant A, Dutton RJ, Khosroheidari M, Green C, da Silva R, Dorrestein PC, Knight R. PMID: 27822524; PMCID: PMC5069746.

View in: PubMed Mentions: 26
The significance of cooking for early hominin scavenging. J Hum Evol. 2015 Jul; 84:62-70. Smith AR, Carmody RN, Dutton RJ, Wrangham RW. PMID: 25962548.

View in: PubMed Mentions: 13 Fields:
Ant Anthropology Bio Biology
Translation:Animals
Fermented foods as experimentally tractable microbial ecosystems. Cell. 2015 Mar 26; 161(1):49-55. Wolfe BE, Dutton RJ. PMID: 25815984.

View in: PubMed Mentions: 104 Fields:
Cel Cell Biology
Translation:Cells PHPublic Health
Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell. 2014 Jul 17; 158(2):422-433. Wolfe BE, Button JE, Santarelli M, Dutton RJ. PMID: 25036636; PMCID: PMC4222527.

View in: PubMed Mentions: 162 Fields:
Cel Cell Biology
Translation:Animals Cells
Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23; 505(7484):559-63. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. PMID: 24336217; PMCID: PMC3957428.

View in: PubMed Mentions: 3414 Fields:
Sci Science
Translation:Humans Cells PHPublic Health CTClinical Trials
Towards an Ecosystem Approach to Cheese Microbiology. Microbiol Spectr. 2013 Oct; 1(1). Wolfe BE, Dutton RJ. PMID: 26184819.

View in: PubMed Mentions: 3 Fields:
Mic Microbiology
Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe. Anal Chem. 2013 Aug 06; 85(15):7014-8. Hsu CC, ElNaggar MS, Peng Y, Fang J, Sanchez LM, Mascuch SJ, M?ller KA, Alazzeh EK, Pikula J, Quinn RA, Zeng Y, Wolfe BE, Dutton RJ, Gerwick L, Zhang L, Liu X, M?nsson M, Dorrestein PC. PMID: 23819546; PMCID: PMC3890442.

View in: PubMed Mentions: 22 Fields:
Che Chemistry Techniques
Translation:Animals Cells
Taking a metagenomic view of human nutrition. Curr Opin Clin Nutr Metab Care. 2012 Sep; 15(5):448-54. Dutton RJ, Turnbaugh PJ. PMID: 22878238.

View in: PubMed Mentions: 19 Fields:
Met Metabolism Nut Nutritional Sciences
Translation:Humans Animals PHPublic Health
Cheese microbes. Curr Biol. 2012 Aug 07; 22(15):R587-9. Button JE, Dutton RJ. PMID: 22877773.

View in: PubMed Mentions: 9 Fields:
Bio Biology
Translation:Animals Cells
Overexpression of the rhodanese PspE, a single cysteine-containing protein, restores disulphide bond formation to an Escherichia coli strain lacking DsbA. Mol Microbiol. 2012 Sep; 85(5):996-1006. Chng SS, Dutton RJ, Denoncin K, Vertommen D, Collet JF, Kadokura H, Beckwith J. PMID: 22809289; PMCID: PMC3429705.

View in: PubMed Mentions: 11 Fields:
Mic Microbiology Mol Molecular Biology
Translation:Cells
A new family of membrane electron transporters and its substrates, including a new cell envelope peroxiredoxin, reveal a broadened reductive capacity of the oxidative bacterial cell envelope. mBio. 2012; 3(2). Cho SH, Parsonage D, Thurston C, Dutton RJ, Poole LB, Collet JF, Beckwith J. PMID: 22493033; PMCID: PMC3322552.

View in: PubMed Mentions: 38 Fields:
Mic Microbiology
Translation:Cells
Direct interaction of FliX and FlbD is required for their regulatory activity in Caulobacter crescentus. BMC Microbiol. 2011 May 02; 11:89. Xu Z, Dutton RJ, Gober JW. PMID: 21535897; PMCID: PMC3096577.

View in: PubMed Mentions: 3 Fields:
Mic Microbiology
Translation:Cells
Membrane topology and mutational analysis of Mycobacterium tuberculosis VKOR, a protein involved in disulfide bond formation and a homologue of human vitamin K epoxide reductase. Antioxid Redox Signal. 2011 Apr 15; 14(8):1413-20. Wang X, Dutton RJ, Beckwith J, Boyd D. PMID: 20969481; PMCID: PMC3061198.

View in: PubMed Mentions: 31 Fields:
Met Metabolism
Translation:Humans Cells
Complete genome sequence of Candidatus Ruthia magnifica. Stand Genomic Sci. 2010 Oct 27; 3(2):163-73. Roeselers G, Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. PMID: 21304746; PMCID: PMC3035367.

View in: PubMed Mentions: 9
Structure of a bacterial homologue of vitamin K epoxide reductase. Nature. 2010 Jan 28; 463(7280):507-12. Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA. PMID: 20110994; PMCID: PMC2919313.

View in: PubMed Mentions: 81 Fields:
Sci Science
Translation:Humans Animals Cells
Inhibition of bacterial disulfide bond formation by the anticoagulant warfarin. Proc Natl Acad Sci U S A. 2010 Jan 05; 107(1):297-301. Dutton RJ, Wayman A, Wei JR, Rubin EJ, Beckwith J, Boyd D. PMID: 20018758; PMCID: PMC2806739.

View in: PubMed Mentions: 28 Fields:
Sci Science
Translation:Humans Animals Cells
Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. Proc Natl Acad Sci U S A. 2008 Aug 19; 105(33):11933-8. Dutton RJ, Boyd D, Berkmen M, Beckwith J. PMID: 18695247; PMCID: PMC2575290.

View in: PubMed Mentions: 124 Fields:
Sci Science
Translation:Cells
Insight into disulfide bond catalysis in Chlamydia from the structure and function of DsbH, a novel oxidoreductase. J Biol Chem. 2008 Jan 11; 283(2):824-32. Mac TT, von Hacht A, Hung KC, Dutton RJ, Boyd D, Bardwell JC, Ulmer TS. PMID: 18003611.

View in: PubMed Mentions: 9 Fields:
Bio Biochemistry
Translation:Humans Cells
Evidence that the SpoIIIE DNA translocase participates in membrane fusion during cytokinesis and engulfment. Mol Microbiol. 2006 Feb; 59(4):1097-113. Liu NJ, Dutton RJ, Pogliano K. PMID: 16430687; PMCID: PMC2885140.

View in: PubMed Mentions: 38 Fields:
Mic Microbiology Mol Molecular Biology
Translation:Cells
Linking structural assembly to gene expression: a novel mechanism for regulating the activity of a sigma54 transcription factor. Mol Microbiol. 2005 Nov; 58(3):743-57. Dutton RJ, Xu Z, Gober JW. PMID: 16238624.

View in: PubMed Mentions: 8 Fields:
Mic Microbiology Mol Molecular Biology
Translation:Cells
The conserved flaF gene has a critical role in coupling flagellin translation and assembly in Caulobacter crescentus. Mol Microbiol. 2005 Aug; 57(4):1127-42. Llewellyn M, Dutton RJ, Easter J, O'donnol D, Gober JW. PMID: 16091049.

View in: PubMed Mentions: 18 Fields:
Mic Microbiology Mol Molecular Biology
Translation:Cells