Publications
For an extensive list of all related publications, please visit Dr. Quinn's Google Scholar Page
2022
Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection
2021
Ghuneim L-AJ, Raghuvanshi R, Neugebauer KA, Guzior D V, Christian MH, Schena B, Feiner JM, Castillo-Bahena A, Mielke J, McClelland M, Conrad D, Klapper I, Zhang T, Quinn RA. 2022. Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection. ISME J. https://doi.org/10.1038/s41396-022-01252-5
A restructuring of microbiome niche space is associated with Elexacaftor-Tezacaftor-Ivacaftor therapy in the cystic fibrosis lung.
Lo M. Sosinski, Christian Martin H, Kerri A. Neugebauer, Lydia-Ann J. Ghuneim, Douglas V. Guzior, Alicia Castillo-Bahena, Jenna Mielke, Ryan Thomas, Marc McClelland, Doug Conrad, Robert A. Quinn. A restructuring of microbiome niche space is associated with Elexacaftor-Tezacaftor-Ivacaftor therapy in the cystic fibrosis lung. Journal of Cystic Fibrosis. 2021
review: microbial transformations of human bile acids
Guzior, D.V. and Robert A. Quinn. Review: microbial transformations of human bile acids. 2021. Microbiome. 9:140.
bridging the gap between analytical and microbial sciences in microbiome research
Quinn. R.A., Hagiwara, K.A., Liu, K., Goudarzi, M., Pathmasiri, W., Sumner, L.W., and Thomas O Metz. Bridging the Gap between Analytical and Microbial Sciences in Microbiome Research. 2021. mSystems. DOI:10.1128/mSystems.00585-21.
metabolomic signatures of coral bleaching history
Roach, T.N.F., Dilworth, J., Martin, C.H., Jones, D.A., Quinn. R.A., and Crawford Drury. Metabolomic signatures of coral bleaching history. 2021. Nature Ecology and Evolution. 5:495-503.
2020
high-resolution longitudinal dynamics of the cystic fibrosis sputum microbiome and metabolome through antibiotic therapy
Raghuvanshi, R., Vasco, K., Vazquez-Baeza, Y., Jiang, L., Morton J.T., Li, D., Gonzalez, A., DeRight Goldasich, L., Humphrey, G., Ackermann, G., Swafford, A.D., Conrad, D., Knight, R., Dorrestein, P.C., and Robert A. Quinn. High-Resolution Longitudional Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome Through Antibiotic Therapy. 2020. mSystems. DOI: 10.1128/mSystems.00292-20.
2019
Microbial transformations of organically fermented foods
Raghuvanshi, R., Grayson, A.G., Schena, I., Amanze, O., Suwintono, K., and R.A. Quinn. Microbial transformations of organically fermented foods. 2019. Metabolites. 9(8):165
Cystic Fibrosis Rapid Response: Translating Multi-omics data into clinically relevant information
Cobian Guemes, A.G., Lim, Y.W., Quinn, R.A., Conrad, D.J., Benler, S., Maughan, H., Edwards, R., Brettin, T., Cantu, V.A., Cuevas, D., Himidi, R., Dorrestein, P. and F. Rohwer. 2019. Cystic Fibrosis Rapid Response: Translating Multi-omics data into clinically relevant information. mBio. 10(2) e00431-19, DOI:10.1128/mBio.00431-19
Neutrophilic proteolysis in the cystic fibrosis lung favors a pathogenic microbiome
Quinn, R.A., Adem, S., Mills, R.H., Comstock, W., DeRight Goldasich, L., Humphrey, G., Aksenov, A.A., Melnik, A.V., da Silva, R., Ackermann, G., Bandeira, N., Gonzalez, D.J., Conrad, D., O’Donoghue, A.J., Knight, R. and P.C. Dorrestein. 2019. Neutrophilic proteolysis in the cystic fibrosis lung favors a pathogenic microbiome. Microbiome. 7:23.
2018
Niche partitioning of a pathogenic microbiome driven by chemical gradients
Quinn, R.A., Comstock, W., Zhang, T., Morton, J.T., da Silva, R., Tran, A., Aksenov, A., Nothias-Scaglia, L., Wangpraseurt, D., Melnik, A.V., Ackerman, G., Conrad, D., Klapper, I., Knight, R., and P.C. Dorrestein. 2018. Niche partitioning of a pathogenic microbiome driven by chemical gradients. Science Advances. 4(9):eeau1908.
Best practices for analyzing microbiomes
Knight, R. Vrbanac, A. Taylor, B.C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., Melnik, A.V., Morton, J.T., Navas, J., Quinn, R.A., Sanders, J.G., Swafford, A.D., Thompson, L.R., Tripathi, A., Xu, Z.Z., Zaneveld, J.R., Zhu, Q., Caporaso, J.G., Dorrestein, P.C. 2018. Best practices for analyzing microbiomes. Nat. Rev. Microbiol. 16:410-422.
Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism
Galtier d'Auriac, I., Quinn, R.A., Maughan, H., Nothias, L-F., Little, M., Kapono, C., Cobian, A., Reyes, B.T., Green, K., Quistad, S.D., Leray, M., Smith, J.E., Dorrestein, P.C., Rohwer, F., Deheyn, D.D., and Aaron C. Hartmann. 2018. Before platelets: the production of platelet activating factor during growth and stress in a basal marine organism. Proceedings of the Royal Society B. 285:4. DOI: 10.1098/rspb.2018.1307
2017
Meta-mass shift chemical (MeMSChem) profiling of metabolomes on coral reefs
Hartmann, A.C., Petras, D., Quinn, R.A., Protsyuk, I., Archer, F.I., Ransome, E.J., Williams, G.J., Bailey, B.A., Vermeij, M.J.A., Alexandrov, T., Dorrestein, P.C., and F. Rohwer. 2017. Meta-mass shift chemical (MeMSChem) profiling of metabolomes on coral reefs. PNAS. doi:10.1073/pnas.1710248114.
Integrating microbiome and metabolome data to understand infectious airway disease
Quinn, R.A.* 2017. Integrating microbiome and metabolome data to understand infectious airway disease. American Journal of Respiratory and Critical Care Medicine. doi.org/10.1164/rccm.201704-0671ED, *corresponding author
The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections
Comstock, W. J., Huh, E., Weekes, R., Watson, C., Xu, T., Dorrestein, P. C., and R.A. Quinn*. 2017. The WinCF Model - An Inexpensive and Tractable Microcosm of a Mucus Plugged Bronchiole to Study the Microbiology of Lung Infections. Journal of Visualized Experiments. (123), e55532, doi.org/10.3791/55532. *corresponding author
Real-time PCR assay for Aquimarina macrocephali subsp. homaria and its distribution in shell disease lesions of Homarus americanus, Milne-Edwards, 1837, and environmental samples
Quinn, R.A., Hazra, A.Y., Smolowitz, R. and A.Y. Chistoserdov. 2017. Real-time PCR assay for Aquimarina macrocephali subsp. homaria and its distribution in shell disease lesions of Homarus americanus, Milne-Edwards, 1837, and environmental samples. Journal of Microbiological Methods. 139:61-67. doi.org/10.1016/j.mimet.2017.04.001
Balance trees provide useful insights into community structure
Morton, J. T., Sanders, J., Quinn, R.A., McDonald, D., Gonzalez, A., Vasquez-Baeza, Y., Navas-Molina, J. A., Hyde, E. R., Song, S. J., Metcalf, J. L., Lladser, M., Dorrestein, P. and R. Knight. 2016. Balance trees provide useful insights into community structure. mSystems. 10.1128/mSystems.00162-16. doi.org/10.1128/mSystems.00162-16
2016
Ecological Networking of Cystic Fibrosis Lung Infections
Quinn, R.A., Whiteson, K., Lim, Y.W., Zhao, J., Conrad, D., LiPuma, J., Rohwer, F. and S. Widder. 2016. Ecological Networking of Cystic Fibrosis Lung Infections. Nature Biofilms and Microbiomes. 2(1):4. doi.org/10.1038/s41522-016-0002-1.
The chemistry associated with built human habitats and transport
Petras, D., Notias, L-F., Quinn, R.A.*, Alexandrov, T., Bandiera, N., Bouslimani, A., Castro-Falcon, G., Chen, L., Dang, T., Dorrestein, P., et al. 2016. The chemistry associated with built human habitats and transport. Analytical Chemistry. 88(22): 10775-10784 *Denotes co-first author.
Mass spectral molecular networking as a pharmaceutical, pharmacological and clinical tool
Quinn, R.A., Nothias, L-F., Vining, O., Meehan, M., Esquenazi, E. and P. Dorrestein. 2016. Mass spectral molecular networking as a pharmaceutical, pharmacological and clinical tool. Trends in Pharmacological Sciences. doi.org/10.1016/j.tips.2016.10.011
Metabolomics of Pulmonary Exacerbations Reveals the Personalized Nature of Cystic Fibrosis Disease
Quinn, R.A., Lim, Y.W., Whiteson, K., Furlan, M., Conrad, D., Rohwer, F. and P. Dorrestein. 2016. Metabolomics of Pulmonary Exacerbations Reveals the Personalized Nature of Cystic Fibrosis Disease. PeerJ. doi.org/10.7717/peerj.2174 Article highlighted here: http://cysticfibrosisnewstoday.com/2016/09/26/
Sharing and community curation of natural products data with Global Natural Products Social molecular networking
Wang, M., Carver, J., Phelan, V., Sanchez, L., Garg, N., Peng, Y., Nguyen, D., Watrous, D., Kapono, C., Luzzatto-Knaan, T., Porto, C., Bouslimani, A., Melnik, A., Meehan, M., Liu, W., Cruesemann, M., Boudreau, P., Esquenazi, E., Sandoval-Calderón, M., Kersten, R., Laura Pace, Quinn, R.A., et. al… W., Moore, B., Dorrestein, P., and Bandiera, N. 2016. Sharing and community curation of natural products data with Global Natural Products Social molecular networking. Nature Biotechnology. 34:828-837. doi.org/10.1038/nbt.3597
Microbiome-wide association studies link dynamic microbial consortia to disease
Gilbert, J., Quinn, R.A., Debelius, J., Xu, Z.Z., Morton, J., Garg, N., Jansson, J., Dorrestein, P. C., and R. Knight. 2016. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 535:94-103. doi.org/10.1038/nature18850.
Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defense
Quinn, R.A., Vermeij, M.A., Hartmann, A.C., Galtier d’Auriac, I., Benler, S., Haas, A., Quistad, S.D., Lim, Y.W., Little, M., Sandin, S., Smith, J.E., Dorrestein, P.C., and F. Rohwer. 2016. Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defense. Proceedings of the Royal Society B. 283:20160469. doi.org/10.1098/rspb.2016.0469 Article highlighted: here1, here2
From sample to multiomics conclusions in under 48 hours
Quinn, R.A., Navas-Molina, J., Hyde, E., Song, S. J., Vazquez-Baeza, Y., Humphrey, G., Gaffney, J., Minich, J. J., Melnik, A. V., Herschend, J., DeReus, J., Durant, A., Dutton, R., Khosroheidari, M., Green, C., da Silva, R., Dorrestein, P.C., and R. Knight. 2016. From sample to multiomics conclusions in under 48 hours. mSystems. 1(2):e00038-16. doi:10.1128/mSystems.00038-16. Article highlighted: here1
Changes in microbial ecology: building predictive understanding of community function and dynamics
Widder, S., Allen, R., Pfeiffer, T., Thomas, C. P., Wiuf, C., Sloan, W. T., Cordero, O., Brown, S., Momeni, B., Shou, W., Kettle, H., Flint, H.J., Haas, A., Laroche, B., Kreft, J., Quinn, R.A., Rainey, P., Isaac Newton Institute Fellows. 2016. Changes in microbial ecology: building predictive understanding of community function and dynamics. ISME J. 10(11):2557-2568. doi.org/10.1038/ismej.2016.45
2015
Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome
Quinn, R.A., Phelan, V. P., Whiteson, K., Garg, N., Bailey, B., Lim, Y.W., Conrad, D., Dorrestein, P.C., and F. Rohwer. 2015. Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. ISME J. 10(6):1483-1498. doi.org/10.1038/ismej.2015.207
Illuminating the dark matter in metabolomics
da Silva, R., Dorrestein, P., and R.A. Quinn. 2015. Illuminating the dark matter in metabolomics. Proceedings of the National Academy of Sciences. 112(41): 12549-12550. doi.org/10.1073/pnas.1516878112
2014
A Winogradsky-based culture system reveals an association between microbial fermentation and cystic fibrosis exacerbation
Quinn, R.A., Whiteson, K., Lim, Y.W., Salamon, P., Bailey, B., Meinardi, S., Sanchez, S., Blake, D., Conrad, D., and F. Rohwer. 2014. A Winogradsky-based culture system reveals an association between microbial fermentation and cystic fibrosis exacerbation. ISME J. 9(4):1024-1038.
The community ecology of microbial molecules
Quinn, R.A. and T. Alexandrov. 2014. The community ecology of microbial molecules. Journal of Chemical Ecology. 40(11):1161-1162.
Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung
Quinn, R.A., Lim, Y.W., Maughan, H., Conrad, D., Rohwer, F and K. L. Whiteson. 2014. Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. mBio. 5(2):e00956-13. doi:10.1128/mBio.00956-13 Article Highlighted in: Molloy, S. 2014. A metabolic milieu. Nat. Rev. Microbiol. 12:315.
The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis patients: parallels from island biogeography
Whiteson, K., Bailey, B., Bergkessel, M., Conrad, D., Delhaes, L., Felts, B., Harris, J.K., Hunter, R., Lim, Y.W., Maughan, H., Quinn, R.A., Salamon, P., Sullivan, J., Wagner, B., and P.B. Rainey. 2014. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis patients: parallels from island biogeography. American Journal of Respiratory and Critical Care Medicine. 189(11):1309-1315.
Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation
Whiteson, K., Meinardi, S., Lim, Y.W., Schmieder, R., Maughan, H., Quinn, R.A., Black, D., Conrad, D., and F. Rohwer. 2014. Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. ISME J. 8:1247-1258.
Pathology of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) in Atlantic Canada
Smolowitz, R., Quinn, R.A., Cawthorn, R.J., Summerfield, R.L. and A. Y. Chistoserdov. 2014. Pathology of two forms of shell disease in the American lobster (Homarus americanus, Milne Edwards) in Atlantic Canada. Journal of Fish Diseases. 37:577-581.