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ArticlesPeer ReviewedFull Text
Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions
Author / Creator:Estaki, Mehrbod ; Pither, Jason ; Baumeister, Peter ; Little, Jonathan P ; Gill, Sandeep K ; Ghosh, Sanjoy ; Ahmadi-Vand, Zahra ; Marsden, Katelyn R ; Gibson, Deanna L
Publisher:England: BioMed Central Ltd
Journal title:Microbiome, 2016-08, Vol.4 (1), p.42-42, Article 42
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Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers
Author / Creator:Zhu, Qiyun ; Hou, Qiangchuan ; Huang, Shi ; Ou, Qianying ; Huo, Dongxue ; Vázquez-Baeza, Yoshiki ; Cen, Chaoping ; Cantu, Victor ; Estaki, Mehrbod ; Chang, Haibo ; Belda-Ferre, Pedro ; Kim, Ho-Cheol ; Chen, Kaining ; Knight, Rob ; Zhang, Jiachao
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2021-11, Vol.15 (11), p.3399-3411
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Fish oil attenuates omega-6 polyunsaturated fatty acid-induced dysbiosis and infectious colitis but impairs LPS dephosphorylation activity causing sepsis
Author / Creator:Ghosh, Sanjoy ; DeCoffe, Daniella ; Brown, Kirsty ; Rajendiran, Ethendhar ; Estaki, Mehrbod ; Dai, Chuanbin ; Yip, Ashley ; Gibson, Deanna L
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-02, Vol.8 (2), p.e55468
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Fish oil supplementation reduces maternal defensive inflammation and predicts a gut bacteriome with reduced immune priming capacity in infants
Author / Creator:Quin, Candice ; Vollman, Deanna M. ; Ghosh, Sanjoy ; Haskey, Natasha ; Estaki, Mehrbod ; Pither, Jason ; Barnett, Jacqueline A. ; Jay, Michael N. ; Birnie, Blake W. ; Gibson, Deanna L.
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2020-08, Vol.14 (8), p.2090-2104
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Author Correction: Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease
Author / Creator:Martinelli, Filippo ; Heinken, Almut ; Henning, Ann-Kristin ; Ulmer, Maria A. ; Hensen, Tim ; González, Antonio ; Arnold, Matthias ; Asthana, Sanjay ; Budde, Kathrin ; Engelman, Corinne D. ; Estaki, Mehrbod ; Grabe, Hans-Jörgen ; Heston, Margo B. ; Johnson, Sterling ; Kastenmüller, Gabi ; Martino, Cameron ; McDonald, Daniel ; Rey, Federico E. ; Kilimann, Ingo ; Peters, Olive ; Wang, Xiao ; Spruth, Eike Jakob ; Schneider, Anja ; Fliessbach, Klaus ; Wiltfang, Jens ; Hansen, Niels ; WenzelGlanz ; Buerger, Katharina ; Janowitz, Daniel ; Laske, Christoph ; Munk, Matthias H. ; Spottke, Annika ; Roy, Nina ; Nauck, Matthias ; Teipel, Stefan ; Knight, Rob ; Kaddurah-Daouk, Rima F. ; Bendlin, Barbara B. ; Hertel, Johannes ; Thiele, Ines
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-11, Vol.14 (1), p.27692-1, Article 27692
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Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome
Author / Creator:Huang, Shi ; Jiang, Shuaiming ; Huo, Dongxue ; Allaband, Celeste ; Estaki, Mehrbod ; Cantu, Victor ; Belda-Ferre, Pedro ; Vázquez-Baeza, Yoshiki ; Zhu, Qiyun ; Ma, Chenchen ; Li, Congfa ; Zarrinpar, Amir ; Liu, Yang-Yu ; Knight, Rob ; Zhang, Jiachao
Publisher:England: BioMed Central
Journal title:Microbiome, 2021-06, Vol.9 (1), p.151-17, Article 151
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Correction to: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers
Author / Creator:Zhu, Qiyun ; Hou, Qiangchuan ; Huang, Shi ; Ou, Qianying ; Huo, Dongxue ; Vázquez-Baeza, Yoshiki ; Cen, Chaoping ; Cantu, Victor ; Estaki, Mehrbod ; Chang, Haibo ; Belda-Ferre, Pedro ; Kim, Ho-Cheol ; Chen, Kaining ; Knight, Rob ; Zhang, Jiachao
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2022-04, Vol.16 (4), p.1201-1201
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ArticlesPeer ReviewedFull Text
Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease
Author / Creator:Martinelli, Filippo ; Heinken, Almut ; Henning, Ann-Kristin ; Ulmer, Maria A. ; Hensen, Tim ; González, Antonio ; Arnold, Matthias ; Asthana, Sanjay ; Budde, Kathrin ; Engelman, Corinne D. ; Estaki, Mehrbod ; Grabe, Hans-Jörgen ; Heston, Margo B. ; Johnson, Sterling ; Kastenmüller, Gabi ; Martino, Cameron ; McDonald, Daniel ; Rey, Federico E. ; Kilimann, Ingo ; Peters, Olive ; Wang, Xiao ; Spruth, Eike Jakob ; Schneider, Anja ; Fliessbach, Klaus ; Wiltfang, Jens ; Hansen, Niels ; Glanz, Wenzel ; Buerger, Katharina ; Janowitz, Daniel ; Laske, Christoph ; Munk, Matthias H. ; Spottke, Annika ; Roy, Nina ; Nauck, Matthias ; Teipel, Stefan ; Knight, Rob ; Kaddurah-Daouk, Rima F. ; Bendlin, Barbara B. ; Hertel, Johannes ; Thiele, Ines
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2024-03, Vol.14 (1), p.6095-14, Article 6095
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ArticlesPeer ReviewedFull Text
Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2−/− Mice
Author / Creator:Estaki, Mehrbod ; Morck, Douglas W ; Ghosh, Sanjoy ; Quin, Candice ; Pither, Jason ; Barnett, Jacqueline A ; Gill, Sandeep K ; Gibson, Deanna L
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2020-10, Vol.5 (5)
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ArticlesPeer ReviewedFull Text
Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils
Author / Creator:Richards, Andrew ; Estaki, Mehrbod ; Úrbez-Torres, José Ramón ; Bowen, Pat ; Lowery, Tom ; Hart, Miranda
Publisher:Basel: MDPI AG
Journal title:Diversity (Basel), 2020-04, Vol.12 (4), p.128
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Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops
Author / Creator:Dillon, Matthew R ; Bolyen, Evan ; Adamov, Anja ; Belk, Aeriel ; Borsom, Emily ; Burcham, Zachary ; Debelius, Justine W ; Deel, Heather ; Emmons, Alex ; Estaki, Mehrbod ; Herman, Chloe ; Keefe, Christopher R ; Morton, Jamie T ; Oliveira, Renato R M ; Sanchez, Andrew ; Simard, Anthony ; Vázquez-Baeza, Yoshiki ; Ziemski, Michal ; Miwa, Hazuki E ; Kerere, Terry A ; Coote, Carline ; Bonneau, Richard ; Knight, Rob ; Oliveira, Guilherme ; Gopalasingam, Piraveen ; Kaehler, Benjamin D ; Cope, Emily K ; Metcalf, Jessica L ; Robeson Ii, Michael S ; Bokulich, Nicholas A ; Caporaso, J Gregory
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2021-06, Vol.17 (6), p.e1009056
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ArticlesPeer ReviewedFull Text
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Author / Creator:Cantrell, Kalen ; Fedarko, Marcus W ; Rahman, Gibraan ; McDonald, Daniel ; Yang, Yimeng ; Zaw, Thant ; Gonzalez, Antonio ; Janssen, Stefan ; Estaki, Mehrbod ; Haiminen, Niina ; Beck, Kristen L ; Zhu, Qiyun ; Sayyari, Erfan ; Morton, James T ; Armstrong, George ; Tripathi, Anupriya ; Gauglitz, Julia M ; Marotz, Clarisse ; Matteson, Nathaniel L ; Martino, Cameron ; Sanders, Jon G ; Carrieri, Anna Paola ; Song, Se Jin ; Swafford, Austin D ; Dorrestein, Pieter C ; Andersen, Kristian G ; Parida, Laxmi ; Kim, Ho-Cheol ; Vázquez-Baeza, Yoshiki ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2021-03, Vol.6 (2)
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ArticlesPeer ReviewedFull Text
High-intensity endurance training results in faster vessel-specific rate of vasorelaxation in type 1 diabetic rats
Author / Creator:Murias, Juan M ; Dey, Adwitia ; Campos, Oscar A ; Estaki, Mehrbod ; Hall, Katharine E ; Melling, Christopher W J ; Noble, Earl G
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-03, Vol.8 (3), p.e59678-e59678
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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases
Author / Creator:Armstrong, George ; Martino, Cameron ; Morris, Justin ; Khaleghi, Behnam ; Kang, Jaeyoung ; DeReus, Jeff ; Zhu, Qiyun ; Roush, Daniel ; McDonald, Daniel ; Gonazlez, Antonio ; Shaffer, Justin P ; Carpenter, Carolina ; Estaki, Mehrbod ; Wandro, Stephen ; Eilert, Sean ; Akel, Ameen ; Eno, Justin ; Curewitz, Ken ; Swafford, Austin D ; Moshiri, Niema ; Rosing, Tajana ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2022-04, Vol.7 (2), p.e0137821-e0137821
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ArticlesPeer ReviewedFull Text
Correction for Estaki et al., “Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2 −/− Mice”
Author / Creator:Estaki, Mehrbod ; Morck, Douglas W. ; Ghosh, Sanjoy ; Quin, Candice ; Pither, Jason ; Barnett, Jacqueline A. ; Gill, Sandeep K. ; Gibson, Deanna L.
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2020-11, Vol.5 (6)
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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Author / Creator:Cantrell, Kalen ; Fedarko, Marcus W. ; Rahman, Gibraan ; McDonald, Daniel ; Yang, Yimeng ; Zaw, Thant ; Gonzalez, Antonio ; Janssen, Stefan ; Estaki, Mehrbod ; Haiminen, Niina ; Beck, Kristen L. ; Zhu, Qiyun ; Sayyari, Erfan ; Morton, James T. ; Armstrong, George ; Tripathi, Anupriya ; Gauglitz, Julia M. ; Marotz, Clarisse ; Matteson, Nathaniel L. ; Martino, Cameron ; Sanders, Jon G. ; Carrieri, Anna Paola ; Song, Se Jin ; Swafford, Austin D. ; Dorrestein, Pieter C. ; Andersen, Kristian G. ; Parida, Laxmi ; Kim, Ho-Cheol ; Vázquez-Baeza, Yoshiki ; Knight, Rob
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2021-04, Vol.6 (2)
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ArticlesPeer ReviewedFull Text
Clinical Consequences of Diet-Induced Dysbiosis
Author / Creator:Chan, Yee Kwan ; Estaki, Mehrbod ; Gibson, Deanna L.
Publisher:Basel, Switzerland: S. Karger AG
Journal title:Annals of nutrition and metabolism, 2013-01, Vol.63 (Suppl 2), p.28-40
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Author / Creator:Bolyen, Evan ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C. Titus ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Da Silva, Ricardo ; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Kosciolek, Tomasz ; Kreps, Jorden ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong-Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Peoples, Samuel L. ; Petras, Daniel ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; van der Hooft, Justin J. J. ; Vargas, Fernando ; von Hippel, Max ; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H. D. ; Willis, Amy D. ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J. Gregory
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2019-08, Vol.37 (8), p.852-857
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ArticlesPeer ReviewedFull Text
North American ginseng protects against muscle damage and reduces neutrophil infiltration after an acute bout of downhill running in rats
Author / Creator:Estaki, Mehrbod ; Noble, Earl G
Publisher:Canada: NRC Research Press
Journal title:Applied physiology, nutrition, and metabolism, 2015-02, Vol.40 (2), p.116-121
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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Author / Creator:Bolyen, Evan ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C. Titus ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Da Silva, Ricardo ; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Kosciolek, Tomasz ; Kreps, Jorden ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong-Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Peoples, Samuel L. ; Petras, Daniel ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; van der Hooft, Justin J. J. ; Vargas, Fernando ; von Hippel, Max ; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H. D. ; Willis, Amy D. ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J. Gregory
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2019-09, Vol.37 (9), p.1091-1091
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Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions

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Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

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Fish oil attenuates omega-6 polyunsaturated fatty acid-induced dysbiosis and infectious colitis but impairs LPS dephosphorylation activity causing sepsis

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Fish oil supplementation reduces maternal defensive inflammation and predicts a gut bacteriome with reduced immune priming capacity in infants

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Author Correction: Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease

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Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

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Correction to: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

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Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease

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Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2−/− Mice

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Cover Crop Diversity as a Tool to Mitigate Vine Decline and Reduce Pathogens in Vineyard Soils

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Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

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High-intensity endurance training results in faster vessel-specific rate of vasorelaxation in type 1 diabetic rats

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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases

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Correction for Estaki et al., “Physical Activity Shapes the Intestinal Microbiome and Immunity of Healthy Mice but Has No Protective Effects against Colitis in MUC2 −/− Mice”

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

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Clinical Consequences of Diet-Induced Dysbiosis

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

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North American ginseng protects against muscle damage and reduces neutrophil infiltration after an acute bout of downhill running in rats

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

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