Journal Article10.1038/S41579-021-00621-9
Mass spectrometry-based metabolomics in microbiome investigations.
Anelize Bauermeister,Helena Mannochio-Russo,Letícia V. Costa-Lotufo,Alan K. Jarmusch,Pieter C. Dorrestein,Pieter C. Dorrestein +5 more
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TL;DR: In this article, the authors provide a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis.
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Abstract: Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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TL;DR: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Structure, function and diversity of the healthy human microbiome
Curtis Huttenhower,Curtis Huttenhower,Dirk Gevers,Rob Knight,Rob Knight,Sahar Abubucker,Jonathan H. Badger,Asif T. Chinwalla,Heather Huot Creasy,Ashlee M. Earl,Michael Fitzgerald,Robert S. Fulton,Michelle G. Giglio,Kymberlie Hallsworth-Pepin,Elizabeth A. Lobos,Ramana Madupu,Vincent Magrini,John Martin,Makedonka Mitreva,Donna M. Muzny,Erica Sodergren,James Versalovic,Aye Wollam,Kim C. Worley,Jennifer R. Wortman,Sarah Young,Qiandong Zeng,Kjersti Aagaard,Olukemi O. Abolude,Emma Allen-Vercoe,Eric J. Alm,Eric J. Alm,Lucia Alvarado,Gary L. Andersen,Scott Anderson,Elizabeth L. Appelbaum,Harindra Arachchi,Gary C. Armitage,Cesar Arze,Tulin Ayvaz,Carl C. Baker,Lisa Begg,Tsegahiwot Belachew,Veena Bhonagiri,Monika Bihan,Martin J. Blaser,Toby Bloom,Vivien Bonazzi,J. Paul Brooks,Gregory A. Buck,Christian J. Buhay,Dana A. Busam,Joseph L. Campbell,Shane Canon,Brandi L. Cantarel,Patrick S. G. Chain,Patrick S. G. Chain,I. Min A. Chen,Lei Chen,Shaila Chhibba,Ken Chu,Dawn Ciulla,Jose C. Clemente,Sandra W. Clifton,Sean Conlan,Jonathan Crabtree,Mary A. Cutting,Noam J. Davidovics,Catherine C. Davis,Todd Z. DeSantis,Carolyn Deal,Kimberley D. Delehaunty,Floyd E. Dewhirst,Elena Deych,Yan Ding,David J. Dooling,Shannon Dugan,Wm. Michael Dunne,Wm. Michael Dunne,A. Scott Durkin,Robert C. Edgar,Rachel L. Erlich,Candace N. Farmer,Ruth M. Farrell,Karoline Faust,Michael Feldgarden,Victor Felix,Sheila Fisher,Anthony A. Fodor,Larry J. Forney,Leslie Foster,Valentina Di Francesco,Jonathan Friedman,Dennis C. Friedrich,Catrina Fronick,Lucinda Fulton,Hongyu Gao,Nathalia Garcia,Georgia Giannoukos,Christina Giblin,Maria Y. Giovanni,Jonathan M. Goldberg,Johannes B. Goll,Antonio Gonzalez,Allison D. Griggs,Sharvari Gujja,Susan Kinder Haake,Brian J. Haas,Holli A. Hamilton,Emily L. Harris,Theresa A. Hepburn,Brandi Herter,Diane E. Hoffmann,Michael Holder,Clinton Howarth,Katherine H. Huang,Susan M. Huse,Jacques Izard,Janet K. Jansson,Huaiyang Jiang,Catherine Jordan,Vandita Joshi,James A. Katancik,Wendy A. Keitel,Scott T. Kelley,Cristyn Kells,Nicholas B. King,Dan Knights,Heidi H. Kong,Omry Koren,Sergey Koren,Karthik Kota,Christie Kovar,Nikos C. Kyrpides,Patricio S. La Rosa,Sandra L. Lee,Katherine P. Lemon,Niall J. Lennon,Cecil M. Lewis,Lora Lewis,Ruth E. Ley,Kelvin Li,Konstantinos Liolios,Bo Liu,Yue Liu,Chien Chi Lo,Catherine A. Lozupone,R. Dwayne Lunsford,Tessa Madden,Anup Mahurkar,Peter J. Mannon,Elaine R. Mardis,Victor M. Markowitz,Victor M. Markowitz,Konstantinos Mavromatis,Jamison McCorrison,Daniel McDonald,Jean E. McEwen,Amy L. McGuire,Pamela McInnes,Teena Mehta,Kathie A. Mihindukulasuriya,Jason R. Miller,Patrick Minx,Irene Newsham,Chad Nusbaum,Michelle Oglaughlin,Joshua Orvis,Ioanna Pagani,Krishna Palaniappan,Shital M. Patel,Matthew D. Pearson,Jane Peterson,Mircea Podar,Craig Pohl,Katherine S. Pollard,Mihai Pop,Margaret Priest,Lita M. Proctor,Xiang Qin,Jeroen Raes,Jacques Ravel,Jeffrey G. Reid,Mina Rho,Rosamond Rhodes,Kevin Riehle,Maria C. Rivera,Beltran Rodriguez-Mueller,Yu-Hui Rogers,Matthew C. Ross,Carsten Russ,Ravi Sanka,Pamela Sankar,J. Fah Sathirapongsasuti,Jeffery A. Schloss,Patrick D. Schloss,Thomas M. Schmidt,Matthew B. Scholz,Lynn M. Schriml,Alyxandria M. Schubert,Nicola Segata,Julia A. Segre,William D. Shannon,Richard R. Sharp,Thomas J. Sharpton,Narmada Shenoy,Nihar U. Sheth,Gina A. Simone,Indresh Singh,Christopher Smillie,Jack D. Sobel,Daniel D. Sommer,Paul Spicer,Granger G. Sutton,Sean M. Sykes,Diana Tabbaa,Mathangi Thiagarajan,Chad Tomlinson,Manolito Torralba,Todd J. Treangen,Rebecca Truty,Tatiana A. Vishnivetskaya,Jason Walker,Lu Wang,Zhengyuan Wang,Doyle V. Ward,Wesley C. Warren,Mark A. Watson,Christopher Wellington,Kris A. Wetterstrand,James R. White,Katarzyna Wilczek-Boney,Yuanqing Wu,Kristine M. Wylie,Todd Wylie,Chandri Yandava,Liang Ye,Yuzhen Ye,Shibu Yooseph,Bonnie P. Youmans,Lan Zhang,Yanjiao Zhou,Yiming Zhu,Laurie Zoloth,Jeremy Zucker,Bruce W. Birren,Richard A. Gibbs,Sarah K. Highlander,Barbara A. Methé,Karen E. Nelson,Joseph F. Petrosino,George M. Weinstock,Richard K. Wilson,Owen White +253 more
TL;DR: The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
Diet rapidly and reproducibly alters the human gut microbiome
Lawrence A. David,Corinne F. Maurice,Rachel N. Carmody,David B. Gootenberg,Julie E. Button,Benjamin E. Wolfe,Alisha V. Ling,A. Sloan Devlin,Yug Varma,Michael A. Fischbach,Sudha B. Biddinger,Rachel J. Dutton,Peter J. Turnbaugh +12 more
TL;DR: Increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease.
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Morgan G. I. Langille,Jesse R. Zaneveld,J. Gregory Caporaso,J. Gregory Caporaso,Daniel McDonald,Dan Knights,Joshua A Reyes,Jose C. Clemente,Deron E. Burkepile,Rebecca Vega Thurber,Rob Knight,Rob Knight,Robert G. Beiko,Curtis Huttenhower,Curtis Huttenhower +14 more
TL;DR: The results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.