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10 results on '"Goldasich, Lindsay DeRight"'

1. Enhancing untargeted metabolomics using metadata-based source annotation

Author

Gauglitz, Julia M, West, Kiana A, Bittremieux, Wout, Williams, Candace L, Weldon, Kelly C, Panitchpakdi, Morgan, Di Ottavio, Francesca, Aceves, Christine M, Brown, Elizabeth, Sikora, Nicole C, Jarmusch, Alan K, Martino, Cameron, Tripathi, Anupriya, Meehan, Michael J, Dorrestein, Kathleen, Shaffer, Justin P, Coras, Roxana, Vargas, Fernando, Goldasich, Lindsay DeRight, Schwartz, Tara, Bryant, MacKenzie, Humphrey, Gregory, Johnson, Abigail J, Spengler, Katharina, Belda-Ferre, Pedro, Diaz, Edgar, McDonald, Daniel, Zhu, Qiyun, Elijah, Emmanuel O, Wang, Mingxun, Marotz, Clarisse, Sprecher, Kate E, Vargas-Robles, Daniela, Withrow, Dana, Ackermann, Gail, Herrera, Lourdes, Bradford, Barry J, Marques, Lucas Maciel Mauriz, Amaral, Juliano Geraldo, Silva, Rodrigo Moreira, Veras, Flavio Protasio, Cunha, Thiago Mattar, Oliveira, Rene Donizeti Ribeiro, Louzada-Junior, Paulo, Mills, Robert H, Piotrowski, Paulina K, Servetas, Stephanie L, Da Silva, Sandra M, Jones, Christina M, Lin, Nancy J, Lippa, Katrice A, Jackson, Scott A, Daouk, Rima Kaddurah, Galasko, Douglas, Dulai, Parambir S, Kalashnikova, Tatyana I, Wittenberg, Curt, Terkeltaub, Robert, Doty, Megan M, Kim, Jae H, Rhee, Kyung E, Beauchamp-Walters, Julia, Wright, Kenneth P, Dominguez-Bello, Maria Gloria, Manary, Mark, Oliveira, Michelli F, Boland, Brigid S, Lopes, Norberto Peporine, Guma, Monica, Swafford, Austin D, Dutton, Rachel J, Knight, Rob, and Dorrestein, Pieter C

Subjects
Medical Biochemistry and Metabolomics, Analytical Chemistry, Biomedical and Clinical Sciences, Chemical Sciences, 2.1 Biological and endogenous factors, Humans, Tandem Mass Spectrometry, Metadata, Metabolomics
Abstract

Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.

Published
2022

2. Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity

Author

Mills, Robert H, Dulai, Parambir S, Vázquez-Baeza, Yoshiki, Sauceda, Consuelo, Daniel, Noëmie, Gerner, Romana R, Batachari, Lakshmi E, Malfavon, Mario, Zhu, Qiyun, Weldon, Kelly, Humphrey, Greg, Carrillo-Terrazas, Marvic, Goldasich, Lindsay DeRight, Bryant, MacKenzie, Raffatellu, Manuela, Quinn, Robert A, Gewirtz, Andrew T, Chassaing, Benoit, Chu, Hiutung, Sandborn, William J, Dorrestein, Pieter C, Knight, Rob, and Gonzalez, David J

Subjects
Microbiology, Biological Sciences, Digestive Diseases, Microbiome, Clinical Research, Crohn's Disease, Inflammatory Bowel Disease, Autoimmune Disease, Nutrition, Precision Medicine, 2.1 Biological and endogenous factors, Oral and gastrointestinal, Adult, Animals, Bacterial Proteins, Bacteroides, Cohort Studies, Colitis, Ulcerative, Feces, Female, Gastrointestinal Microbiome, Humans, Longitudinal Studies, Male, Metagenome, Metagenomics, Mice, Middle Aged, Peptide Hydrolases, Proteomics, Severity of Illness Index, Medical Microbiology
Abstract

Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.

Published
2022

3. Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation

Author

Gauglitz, Julia M., West, Kiana A., Bittremieux, Wout, Williams, Candace L., Weldon, Kelly C., Panitchpakdi, Morgan, Di Ottavio, Francesca, Aceves, Christine M., Brown, Elizabeth, Sikora, Nicole C., Jarmusch, Alan K., Martino, Cameron, Tripathi, Anupriya, Meehan, Michael J., Dorrestein, Kathleen, Shaffer, Justin P., Coras, Roxana, Vargas, Fernando, Goldasich, Lindsay DeRight, Schwartz, Tara, Bryant, MacKenzie, Humphrey, Gregory, Johnson, Abigail J., Spengler, Katharina, Belda-Ferre, Pedro, Diaz, Edgar, McDonald, Daniel, Zhu, Qiyun, Elijah, Emmanuel O., Wang, Mingxun, Marotz, Clarisse, Sprecher, Kate E., Vargas-Robles, Daniela, Withrow, Dana, Ackermann, Gail, Herrera, Lourdes, Bradford, Barry J., Marques, Lucas Maciel Mauriz, Amaral, Juliano Geraldo, Silva, Rodrigo Moreira, Veras, Flavio Protasio, Cunha, Thiago Mattar, Oliveira, Rene Donizeti Ribeiro, Louzada-Junior, Paulo, Mills, Robert H., Piotrowski, Paulina K., Servetas, Stephanie L., Da Silva, Sandra M., Jones, Christina M., Lin, Nancy J., Lippa, Katrice A., Jackson, Scott A., Daouk, Rima Kaddurah, Galasko, Douglas, Dulai, Parambir S., Kalashnikova, Tatyana I., Wittenberg, Curt, Terkeltaub, Robert, Doty, Megan M., Kim, Jae H., Rhee, Kyung E., Beauchamp-Walters, Julia, Wright, Jr, Kenneth P., Dominguez-Bello, Maria Gloria, Manary, Mark, Oliveira, Michelli F., Boland, Brigid S., Lopes, Norberto Peporine, Guma, Monica, Swafford, Austin D., Dutton, Rachel J., Knight, Rob, and Dorrestein, Pieter C.

Published
2023
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4. American Gut: an Open Platform for Citizen Science Microbiome Research

Author

McDonald, Daniel, Hyde, Embriette, Debelius, Justine W, Morton, James T, Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A, Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, Goldasich, Lindsay DeRight, Dorrestein, Pieter C, Dunn, Robert R, Fahimipour, Ashkaan K, Gaffney, James, Gilbert, Jack A, Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A, Janssen, Stefan, Jeste, Dilip V, Jiang, Lingjing, Kelley, Scott T, Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V, Metcalf, Jessica L, Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T, Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S, Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Jin, Spector, Timothy, Swafford, Austin D, Thackray, Varykina G, Thompson, Luke R, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, Mann, Allison E, Amir, Amnon, Frazier, Angel, Martino, Cameron, Lebrilla, Carlito, Lozupone, Catherine, Lewis, Cecil M, Raison, Charles, Zhang, Chi, Lauber, Christian L, Warinner, Christina, Lowry, Christopher A, Callewaert, Chris, Bloss, Cinnamon, Willner, Dana, Galzerani, Daniela Domingos, Gonzalez, David J, Mills, David A, Chopra, Deepak, Gevers, Dirk, Berg-Lyons, Donna, Sears, Dorothy D, Wendel, Doug, Lovelace, Elijah, Pierce, Emily, TerAvest, Emily, Bolyen, Evan, Bushman, Frederic D, Wu, Gary D, Church, George M, Saxe, Gordon, Holscher, Hanna D, Ugrina, Ivo, German, J Bruce, Caporaso, J Gregory, Wozniak, Jacob M, Kerr, Jacqueline, Ravel, Jacques, Lewis, James D, Suchodolski, Jan S, Jansson, Janet K, Hampton-Marcell, Jarrad T, and Bobe, Jason

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Medical Biochemistry and Metabolomics, Human Genome, Microbiome, Genetics, Clinical Research, 4.1 Discovery and preclinical testing of markers and technologies, citizen science, microbiome, American Gut Consortium
Abstract

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

Published
2018

5. Reference data-set driven metabolomics

Author

Gauglitz, Julia, primary, West, Kiana, additional, Bittremieux, Wout, additional, Williams, Candace, additional, Weldon, Kelly, additional, Panitchpakdi, Morgan, additional, Diottavio, Francesca, additional, Aceves, Christine, additional, Brown, Elizabeth, additional, Sikora, Nicole, additional, Jarmusch, Alan, additional, Martino, Cameron, additional, Tripathi, Anupriya, additional, Meehan, Michael, additional, Dorrestein, Kathleen, additional, Shaffer, Justin, additional, Coras, Roxana, additional, Vargas, Fernando, additional, Goldasich, Lindsay DeRight, additional, Schwartz, Tara, additional, Bryant, MacKenzie, additional, Humphrey, Greg, additional, Johnson, Abigail, additional, Spengler, Katharina, additional, Belda-Ferre, Pedro, additional, Diaz, Edgar, additional, McDonald, Daniel, additional, Zhu, Qiyun, additional, Emmanuel, Elijah, additional, Wang, Mingxun, additional, Marotz, Clarisse, additional, Sprecher, Kate, additional, RObles, Daniela Vargas, additional, Withrow, Dana, additional, Ackermann, Gail, additional, Herrera, Lourdes, additional, Bradford, Barry, additional, Marques, Lucas Maciel Mauriz, additional, Amaral, Juliano Geraldo, additional, Silva, Rodrigo Moreira, additional, Veras, Flávio Protaso, additional, Cunha, Thiago Mattar, additional, Oliveira, Rene Donizeti Ribeiro, additional, Louzada-Junior, Paulo, additional, Mills, Robert, additional, Piotrowski, Paulina, additional, Servetas, Stephanie, additional, DaSilva, Sandra, additional, Jones, Christina, additional, Lin, Nancy, additional, Lippa, Katrice, additional, Jackson, Scott, additional, Daouk, Rima Kaddurah, additional, Galasko, Douglas, additional, Dulai, Parambir, additional, Kalashnikova, Tatyana, additional, Wittenberg, Curt, additional, Gonzalez, David, additional, Terkeltaub, Robert, additional, Doty, Megan, additional, Kim, Jae, additional, Rhee, Kyung, additional, Beauchamp-Walters, Julia, additional, Wright, Kenneth, additional, Dominguez-Bello, Maria Gloria, additional, Manery, Mark, additional, Oliveira, Michelli, additional, Boland, Brigid, additional, Lopes, Norberto, additional, Guma, Monica, additional, Swafford, Austin, additional, Dutton, Rachel, additional, Knight, Rob, additional, and Dorrestein, Pieter, additional

Published
2021
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6. Reference data based insights expand understanding of human metabolomes

Author

Gauglitz, Julia M., primary, Bittremieux, Wout, additional, Williams, Candace L., additional, Weldon, Kelly C., additional, Panitchpakdi, Morgan, additional, Di Ottavio, Francesca, additional, Aceves, Christine M., additional, Brown, Elizabeth, additional, Sikora, Nicole C., additional, Jarmusch, Alan K., additional, Martino, Cameron, additional, Tripathi, Anupriya, additional, Sayyari, Erfan, additional, Shaffer, Justin P., additional, Coras, Roxana, additional, Vargas, Fernando, additional, Goldasich, Lindsay DeRight, additional, Schwartz, Tara, additional, Bryant, MacKenzie, additional, Humphrey, Gregory, additional, Johnson, Abigail J., additional, Spengler, Katharina, additional, Belda-Ferre, Pedro, additional, Diaz, Edgar, additional, McDonald, Daniel, additional, Zhu, Qiyun, additional, Nguyen, Dominic S., additional, Elijah, Emmanuel O., additional, Wang, Mingxun, additional, Marotz, Clarisse, additional, Sprecher, Kate E., additional, Robles, Daniela Vargas, additional, Withrow, Dana, additional, Ackermann, Gail, additional, Herrera, Lourdes, additional, Bradford, Barry J., additional, Mauriz Marques, Lucas Maciel, additional, Amaral, Juliano Geraldo, additional, Silva, Rodrigo Moreira, additional, Veras, Flávio Protaso, additional, Cunha, Thiago Mattar, additional, Ribeiro Oliveira, Rene Donizeti, additional, Louzada-Junior, Paulo, additional, Mills, Robert H., additional, Galasko, Douglas, additional, Dulai, Parambir S., additional, Wittenberg, Curt, additional, Gonzalez, David J., additional, Terkeltaub, Robert, additional, Doty, Megan M., additional, Kim, Jae H., additional, Rhee, Kyung E., additional, Beauchamp-Walters, Julia, additional, Wright, Kenneth P., additional, Dominguez-Bello, Maria Gloria, additional, Manary, Mark, additional, Oliveira, Michelli F., additional, Boland, Brigid S., additional, Lopes, Norberto Peporine, additional, Guma, Monica, additional, Swafford, Austin D., additional, Dutton, Rachel J., additional, Knight, Rob, additional, and Dorrestein, Pieter C., additional

Published
2020
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7. Additional file 2 of Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

Author

Quinn, Robert, Adem, Sandeep, Mills, Robert, Comstock, William, Goldasich, Lindsay DeRight, Humphrey, Gregory, Aksenov, Alexander, Melnik, Alexei, Silva, Ricardo, Ackermann, Gail, Bandeira, Nuno, Gonzalez, David, Conrad, Doug, O’Donoghue, Anthony, Knight, Rob, and Dorrestein, Pieter

Subjects
3. Good health
Abstract

á Supplementary methods. Description of mass spectrometry data processing (DOCX 23 kb)

9. Additional file 2 of Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome

Author

Quinn, Robert, Adem, Sandeep, Mills, Robert, Comstock, William, Goldasich, Lindsay DeRight, Humphrey, Gregory, Aksenov, Alexander, Melnik, Alexei, Silva, Ricardo, Ackermann, Gail, Bandeira, Nuno, Gonzalez, David, Conrad, Doug, O’Donoghue, Anthony, Knight, Rob, and Dorrestein, Pieter

Subjects
3. Good health
Abstract

á Supplementary methods. Description of mass spectrometry data processing (DOCX 23 kb)

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