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Items: 1 to 50 of 299

1.

Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: a Pharmacokinetic, Microbiome and Untargeted Metabolomics Study.

Jarmusch AK, Vrbanac A, Momper JD, Ma JD, Alhaja M, Liyanage M, Knight R, Dorrestein PC, Tsunoda SM.

Clin Transl Sci. 2020 Mar 26. doi: 10.1111/cts.12785. [Epub ahead of print]

PMID:
32216086
2.

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome.

Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R.

mSystems. 2020 Mar 17;5(2). pii: e00901-19. doi: 10.1128/mSystems.00901-19.

3.

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs.

Gauglitz JM, Morton JT, Tripathi A, Hansen S, Gaffney M, Carpenter C, Weldon KC, Shah R, Parampil A, Fidgett AL, Swafford AD, Knight R, Dorrestein PC.

mSystems. 2020 Mar 10;5(2). pii: e00635-19. doi: 10.1128/mSystems.00635-19.

4.

Emerging Priorities for Microbiome Research.

Cullen CM, Aneja KK, Beyhan S, Cho CE, Woloszynek S, Convertino M, McCoy SJ, Zhang Y, Anderson MZ, Alvarez-Ponce D, Smirnova E, Karstens L, Dorrestein PC, Li H, Sen Gupta A, Cheung K, Powers JG, Zhao Z, Rosen GL.

Front Microbiol. 2020 Feb 19;11:136. doi: 10.3389/fmicb.2020.00136. eCollection 2020. Review.

5.

Dietary prebiotics alter novel microbial dependent fecal metabolites that improve sleep.

Thompson RS, Vargas F, Dorrestein PC, Chichlowski M, Berg BM, Fleshner M.

Sci Rep. 2020 Mar 2;10(1):3848. doi: 10.1038/s41598-020-60679-y.

6.

Global chemical effects of the microbiome include new bile-acid conjugations.

Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC.

Nature. 2020 Mar;579(7797):123-129. doi: 10.1038/s41586-020-2047-9. Epub 2020 Feb 26.

PMID:
32103176
7.

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome.

Bowers SJ, Vargas F, González A, He S, Jiang P, Dorrestein PC, Knight R, Wright KP Jr, Lowry CA, Fleshner M, Vitaterna MH, Turek FW.

PLoS One. 2020 Feb 20;15(2):e0229001. doi: 10.1371/journal.pone.0229001. eCollection 2020.

8.

Assessing specialized metabolite diversity of Alnus species by a digitized LC-MS/MS data analysis workflow.

Kang KB, Woo S, Ernst M, van der Hooft JJJ, Nothias LF, da Silva RR, Dorrestein PC, Sung SH, Lee M.

Phytochemistry. 2020 Feb 12;173:112292. doi: 10.1016/j.phytochem.2020.112292. [Epub ahead of print]

PMID:
32062198
9.

A Convolutional Neural Network-Based Approach for the Rapid Annotation of Molecularly Diverse Natural Products.

Reher R, Kim HW, Zhang C, Mao HH, Wang M, Nothias LF, Caraballo-Rodriguez AM, Glukhov E, Teke B, Leao T, Alexander KL, Duggan BM, Van Everbroeck EL, Dorrestein PC, Cottrell GW, Gerwick WH.

J Am Chem Soc. 2020 Mar 4;142(9):4114-4120. doi: 10.1021/jacs.9b13786. Epub 2020 Feb 21.

PMID:
32045230
10.

Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau.

Maloney KN, Botts RT, Davis TS, Okada BK, Maloney EM, Leber CA, Alvarado O, Brayton C, Caraballo-Rodríguez AM, Chari JV, Chicoine B, Crompton JC, Davis SR, Gromek SM, Kurnianda V, Quach K, Samples RM, Shieh V, Sultana CM, Tanaka J, Dorrestein PC, Balunas MJ, McFadden CS.

J Nat Prod. 2020 Mar 27;83(3):693-705. doi: 10.1021/acs.jnatprod.9b01128. Epub 2020 Jan 23.

PMID:
31971803
11.

Protocol for Community-created Public MS/MS Reference Spectra Within the Global Natural Products Social Molecular Networking Infrastructure.

Vargas F, Weldon KC, Sikora N, Wang M, Zhang Z, Gentry EC, Panitchpakdi MW, Caraballo-Rodríguez AM, Dorrestein PC, Jarmusch AK.

Rapid Commun Mass Spectrom. 2020 Jan 13:e8725. doi: 10.1002/rcm.8725. [Epub ahead of print]

PMID:
31930757
12.

A UHPLC-HRMS based metabolomics and chemoinformatics approach to chemically distinguish 'super foods' from a variety of plant-based foods.

Di Ottavio F, Gauglitz JM, Ernst M, Panitchpakdi MW, Fanti F, Compagnone D, Dorrestein PC, Sergi M.

Food Chem. 2020 May 30;313:126071. doi: 10.1016/j.foodchem.2019.126071. Epub 2019 Dec 24.

PMID:
31927204
13.

Mass spectrometry searches using MASST.

Wang M, Jarmusch AK, Vargas F, Aksenov AA, Gauglitz JM, Weldon K, Petras D, da Silva R, Quinn R, Melnik AV, van der Hooft JJJ, Caraballo-Rodríguez AM, Nothias LF, Aceves CM, Panitchpakdi M, Brown E, Di Ottavio F, Sikora N, Elijah EO, Labarta-Bajo L, Gentry EC, Shalapour S, Kyle KE, Puckett SP, Watrous JD, Carpenter CS, Bouslimani A, Ernst M, Swafford AD, Zúñiga EI, Balunas MJ, Klassen JL, Loomba R, Knight R, Bandeira N, Dorrestein PC.

Nat Biotechnol. 2020 Jan;38(1):23-26. doi: 10.1038/s41587-019-0375-9. No abstract available.

PMID:
31894142
14.

De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments.

Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA.

Cell Syst. 2020 Jan 22;10(1):99-108.e5. doi: 10.1016/j.cels.2019.11.007. Epub 2019 Dec 18.

PMID:
31864964
15.

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media.

Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J.

Sci Data. 2019 Dec 17;6(1):322. doi: 10.1038/s41597-019-0331-z.

16.

The Microbiome and Its Potential for Pharmacology.

Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R.

Handb Exp Pharmacol. 2019;260:301-326. doi: 10.1007/164_2019_317. Review.

PMID:
31820171
17.

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery.

van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, Neto FC, Castaño-Espriu L, Chang C, Clark TN, Cleary Little JL, Delgadillo DA, Dorrestein PC, Duncan KR, Egan JM, Galey MM, Haeckl FPJ, Hua A, Hughes AH, Iskakova D, Khadilkar A, Lee JH, Lee S, LeGrow N, Liu DY, Macho JM, McCaughey CS, Medema MH, Neupane RP, O'Donnell TJ, Paula JS, Sanchez LM, Shaikh AF, Soldatou S, Terlouw BR, Tran TA, Valentine M, van der Hooft JJJ, Vo DA, Wang M, Wilson D, Zink KE, Linington RG.

ACS Cent Sci. 2019 Nov 27;5(11):1824-1833. doi: 10.1021/acscentsci.9b00806. Epub 2019 Nov 14.

18.

Comparative Genomics and Metabolomics Analyses of Clavulanic Acid-Producing Streptomyces Species Provides Insight Into Specialized Metabolism.

AbuSara NF, Piercey BM, Moore MA, Shaikh AA, Nothias LF, Srivastava SK, Cruz-Morales P, Dorrestein PC, Barona-Gómez F, Tahlan K.

Front Microbiol. 2019 Nov 8;10:2550. doi: 10.3389/fmicb.2019.02550. eCollection 2019.

19.

Interleukin-17 Inhibition in Spondyloarthritis Is Associated With Subclinical Gut Microbiome Perturbations and a Distinctive Interleukin-25-Driven Intestinal Inflammation.

Manasson J, Wallach DS, Guggino G, Stapylton M, Badri MH, Solomon G, Reddy SM, Coras R, Aksenov AA, Jones DR, Girija PV, Neimann AL, Heguy A, Segal LN, Dorrestein PC, Bonneau R, Guma M, Ciccia F, Ubeda C, Clemente JC, Scher JU.

Arthritis Rheumatol. 2019 Nov 14. doi: 10.1002/art.41169. [Epub ahead of print]

PMID:
31729183
20.

Learning representations of microbe-metabolite interactions.

Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R.

Nat Methods. 2019 Dec;16(12):1306-1314. doi: 10.1038/s41592-019-0616-3. Epub 2019 Nov 4.

21.

Home chemical and microbial transitions across urbanization.

McCall LI, Callewaert C, Zhu Q, Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG.

Nat Microbiol. 2020 Jan;5(1):108-115. doi: 10.1038/s41564-019-0593-4. Epub 2019 Nov 4.

PMID:
31686026
22.

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads.

Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R.

Genome Biol. 2019 Oct 31;20(1):226. doi: 10.1186/s13059-019-1834-9.

23.

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.

Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H.

Cell Syst. 2019 Dec 18;9(6):600-608.e4. doi: 10.1016/j.cels.2019.09.004. Epub 2019 Oct 16.

PMID:
31629686
24.

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N.

mSystems. 2019 Sep 24;4(5). pii: e00375-19. doi: 10.1128/mSystems.00375-19.

25.

Cytotoxic Microcolin Lipopeptides from the Marine Cyanobacterium Moorea producens.

Yu HB, Glukhov E, Li Y, Iwasaki A, Gerwick L, Dorrestein PC, Jiao BH, Gerwick WH.

J Nat Prod. 2019 Sep 27;82(9):2608-2619. doi: 10.1021/acs.jnatprod.9b00549. Epub 2019 Aug 30.

PMID:
31468974
26.

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages.

Gauglitz JM, Aceves CM, Aksenov AA, Aleti G, Almaliti J, Bouslimani A, Brown EA, Campeau A, Caraballo-Rodríguez AM, Chaar R, da Silva RR, Demko AM, Di Ottavio F, Elijah E, Ernst M, Ferguson LP, Holmes X, Jarmusch AK, Jiang L, Kang KB, Koester I, Kwan B, Li J, Li Y, Melnik AV, Molina-Santiago C, Ni B, Oom AL, Panitchpakdi MW, Petras D, Quinn R, Sikora N, Spengler K, Teke B, Tripathi A, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vrbanac A, Vu AQ, Wang SC, Weldon K, Wilson K, Wozniak JM, Yoon M, Bandeira N, Dorrestein PC.

Food Chem. 2020 Jan 1;302:125290. doi: 10.1016/j.foodchem.2019.125290. Epub 2019 Jul 30.

PMID:
31404873
27.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
28.

Perspective: Dietary Biomarkers of Intake and Exposure-Exploration with Omics Approaches.

Maruvada P, Lampe JW, Wishart DS, Barupal D, Chester DN, Dodd D, Djoumbou-Feunang Y, Dorrestein PC, Dragsted LO, Draper J, Duffy LC, Dwyer JT, Emenaker NJ, Fiehn O, Gerszten RE, B Hu F, Karp RW, Klurfeld DM, Laughlin MR, Little AR, Lynch CJ, Moore SC, Nicastro HL, O'Brien DM, Ordovás JM, Osganian SK, Playdon M, Prentice R, Raftery D, Reisdorph N, Roche HM, Ross SA, Sang S, Scalbert A, Srinivas PR, Zeisel SH.

Adv Nutr. 2020 Mar 1;11(2):200-215. doi: 10.1093/advances/nmz075.

PMID:
31386148
29.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

30.

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L.

Ernst M, Nothias LF, van der Hooft JJJ, Silva RR, Saslis-Lagoudakis CH, Grace OM, Martinez-Swatson K, Hassemer G, Funez LA, Simonsen HT, Medema MH, Staerk D, Nilsson N, Lovato P, Dorrestein PC, Rønsted N.

Front Plant Sci. 2019 Jul 2;10:846. doi: 10.3389/fpls.2019.00846. eCollection 2019.

31.

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools.

Ernst M, Kang KB, Caraballo-Rodríguez AM, Nothias LF, Wandy J, Chen C, Wang M, Rogers S, Medema MH, Dorrestein PC, van der Hooft JJJ.

Metabolites. 2019 Jul 16;9(7). pii: E144. doi: 10.3390/metabo9070144.

32.

Early-Career Scientists Shaping the World.

Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J.

mSystems. 2019 May 7;4(3). pii: e00196-19. doi: 10.1128/mSystems.00196-19. No abstract available.

33.

The impact of skin care products on skin chemistry and microbiome dynamics.

Bouslimani A, da Silva R, Kosciolek T, Janssen S, Callewaert C, Amir A, Dorrestein K, Melnik AV, Zaramela LS, Kim JN, Humphrey G, Schwartz T, Sanders K, Brennan C, Luzzatto-Knaan T, Ackermann G, McDonald D, Zengler K, Knight R, Dorrestein PC.

BMC Biol. 2019 Jun 12;17(1):47. doi: 10.1186/s12915-019-0660-6.

34.

Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation.

Nothias-Esposito M, Nothias LF, Da Silva RR, Retailleau P, Zhang Z, Leyssen P, Roussi F, Touboul D, Paolini J, Dorrestein PC, Litaudon M.

J Nat Prod. 2019 Jun 28;82(6):1459-1470. doi: 10.1021/acs.jnatprod.8b00916. Epub 2019 Jun 5.

PMID:
31181921
35.

Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin.

Jarmusch AK, Elijah EO, Vargas F, Bouslimani A, da Silva RR, Ernst M, Wang M, Del Rosario KK, Dorrestein PC, Tsunoda SM.

Anal Chem. 2019 Jul 2;91(13):8062-8069. doi: 10.1021/acs.analchem.8b05854. Epub 2019 Jun 10.

PMID:
31074958
36.

Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment.

Sprecher KE, Ritchie HK, Burke TM, Depner CM, Smits AN, Dorrestein PC, Fleshner M, Knight R, Lowry CA, Turek FW, Vitaterna MH, Wright KP.

Sleep. 2019 Aug 1;42(8). pii: zsz113. doi: 10.1093/sleep/zsz113.

PMID:
31070769
37.

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems.

Tripathi A, Xu ZZ, Xue J, Poulsen O, Gonzalez A, Humphrey G, Meehan MJ, Melnik AV, Ackermann G, Zhou D, Malhotra A, Haddad GG, Dorrestein PC, Knight R.

mSystems. 2019 Apr 30;4(2). pii: e00058-19. doi: 10.1128/mSystems.00058-19. eCollection 2019 Mar-Apr.

38.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
39.

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media.

Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM.

Sci Data. 2019 Apr 26;6(1):43. doi: 10.1038/s41597-019-0051-4.

40.

The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization.

Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, García-Martín ML, Lamon G, Haberstein B, Cazorla FM, de Vicente A, Loquet A, Dorrestein PC, Romero D.

Nat Commun. 2019 Apr 23;10(1):1919. doi: 10.1038/s41467-019-09944-x.

41.

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease.

Aleti G, Baker JL, Tang X, Alvarez R, Dinis M, Tran NC, Melnik AV, Zhong C, Ernst M, Dorrestein PC, Edlund A.

mBio. 2019 Apr 16;10(2). pii: e00321-19. doi: 10.1128/mBio.00321-19.

42.

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information.

Dührkop K, Fleischauer M, Ludwig M, Aksenov AA, Melnik AV, Meusel M, Dorrestein PC, Rousu J, Böcker S.

Nat Methods. 2019 Apr;16(4):299-302. doi: 10.1038/s41592-019-0344-8. Epub 2019 Mar 18.

PMID:
30886413
43.

Heavy metal exposure causes changes in the metabolic health-associated gut microbiome and metabolites.

Li X, Brejnrod AD, Ernst M, Rykær M, Herschend J, Olsen NMC, Dorrestein PC, Rensing C, Sørensen SJ.

Environ Int. 2019 May;126:454-467. doi: 10.1016/j.envint.2019.02.048. Epub 2019 Mar 4.

44.

Viscosin-like lipopeptides from frog skin bacteria inhibit Aspergillus fumigatus and Batrachochytrium dendrobatidis detected by imaging mass spectrometry and molecular networking.

Martin H C, Ibáñez R, Nothias LF, Boya P CA, Reinert LK, Rollins-Smith LA, Dorrestein PC, Gutiérrez M.

Sci Rep. 2019 Feb 28;9(1):3019. doi: 10.1038/s41598-019-39583-7.

45.

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae.

Kang KB, Ernst M, van der Hooft JJJ, da Silva RR, Park J, Medema MH, Sung SH, Dorrestein PC.

Plant J. 2019 Jun;98(6):1134-1144. doi: 10.1111/tpj.14292. Epub 2019 Mar 25.

PMID:
30786088
46.

Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor.

Luzzatto-Knaan T, Melnik AV, Dorrestein PC.

ACS Chem Biol. 2019 Mar 15;14(3):459-467. doi: 10.1021/acschembio.8b01120. Epub 2019 Feb 22.

PMID:
30763059
47.

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome.

Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC.

Microbiome. 2019 Feb 13;7(1):23. doi: 10.1186/s40168-019-0636-3.

48.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

PMID:
30679363
49.

Lugdunomycin, an Angucycline-Derived Molecule with Unprecedented Chemical Architecture.

Wu C, van der Heul HU, Melnik AV, Lübben J, Dorrestein PC, Minnaard AJ, Choi YH, van Wezel GP.

Angew Chem Int Ed Engl. 2019 Feb 25;58(9):2809-2814. doi: 10.1002/anie.201814581. Epub 2019 Jan 29.

50.

Dereplication of microbial metabolites through database search of mass spectra.

Mohimani H, Gurevich A, Shlemov A, Mikheenko A, Korobeynikov A, Cao L, Shcherbin E, Nothias LF, Dorrestein PC, Pevzner PA.

Nat Commun. 2018 Oct 2;9(1):4035. doi: 10.1038/s41467-018-06082-8.

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