Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

Tal Korem*, David Zeevi*, Jotham Suez*, Adina Weinberger*, Tali Avnit-Sagi, Maya Pompan-Lotan, Elad Matot, Ghil Jona, Alon Harmelin, Nadav Cohen, Alexandra Sirota-Madi, Christoph A Thaiss, Meirav Pevsner-Fischer, Rotem Sorek, Ramnik J Xavier, Eran Elinav, Eran Segal.

Science 349 (6252), 1101-1106 (2015)

Coverage: Nature Reviews Microbiology highlight, Science perspective

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome

William F. Kindschuh*, Federico Baldini*, Martin C. Liu*, Kristin D. Gerson, Jingqiu Liao, Harry H. Lee, Lauren Anton, Pawel Gajer, Jacques Ravel, Maayan Levy, Michal A. Elovitz, Tal Korem†.

bioRxiv (2021)

The gut microbiome of adults with type 1 diabetes and its association with the host glycemic control

Smadar Shilo, Anastasia Godneva, Marianna Rachmiel, Tal Korem, Yuval Bussi, Dmitry Kolobkov, Tal Karady, Noam Bar, Bat Chen Wolf, Yitav Glantz-Gashai, Michal Cohen, Nehama Zuckerman Levin, Naim Shehadeh, Noah Gruber, Neriya Levran, Shlomit Koren, Adina Weinberger, Orit Pinhas-Hamiel, Eran Segal.

Diabetes Care, dc211656 (2022)

​

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates

Tyler A Joseph, Philippe Chlenski, Aviya Litman, Tal Korem†, Itsik Pe'er†.

Genome Research 32: 558-568 (2022)

​

A non-optimal cervicovaginal microbiota in pregnancy is associated with a distinct metabolomic signature among non-Hispanic Black individuals

Kristin D Gerson, Jingqiu Liao, Clare McCarthy, Heather H Burris, Tal Korem, Maayan Levy, Jacques Ravel, Michal A Elovitz

Scientific Reports 11, 22794 (2021)

​

Prediction of personal glycemic responses to food for individuals with type 1 diabetes through integration of clinical and microbial data

Smadar Shilo, Anastasia Godneva, Marianna Rachmiel, Tal Korem, Dmitry Kolobkov, Tal Karady, Noam Bar, Bat Chen Wolf, Yitav Glantz-Gashai, Michal Cohen, Nehama Zuckerman Levin, Naim Shehadeh, Noah Gruber, Neriya Levran, Shlomit Koren, Adina Weinberger, Orit Pinhas-Hamiel, Eran Segal.

Diabetes Care, dc211048 (2021)

​

Embracing metagenomic complexity with a genome-free approach

Izaak Coleman, Tal Korem†.

mSystems 6(4), e00816-21 (2021) [Commentary]

​

Minimal associations between short-term dietary intake and salivary microbiome composition

Judith Kim, Minyi Lee , Brittany Baldwin-Hunter, Quinn S Solfisburg, Charles J Lightdale, Tal Korem, Chin Hur, Julian A Abrams.

Microorganisms 9(8), 1739 (2021)

​

Deciphering metabolism, one microbe at a time

William F Kindschuh, Tal Korem†.

Nature 595, 355-357 (2021) [News & Views]

​

The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome

B Brett Finlay, Katherine R Amato, Meghan Azad, Martin J Blaser, Thomas CG Bosch, Hiutung Chu, Maria Gloria Dominguez-Bello, Stanislav Dusko Ehrlich, Eran Elinav, Naama Geva-Zatorsky, Philippe Gros, Karen Guillemin, Frédéric Keck, Tal Korem, Margaret J McFall-Ngai, Melissa K Melby, Mark Nichter, Sven Pettersson, Hendrik Poinar, Tobias Rees, Carolina Tropini, Liping Zhao, Tamara Giles-Vernick

Proceedings of the National Academy of Sciences 118(6) (2021)

​

Relationship of the esophageal microbiome and tissue gene expression and links to the oral microbiome: a randomized clinical trial

Medini K Annavajhala, Michael May, Griselda Compres, Daniel E Freedberg, Roseanna Graham, Stephania Stump, Jianwen Que, Tal Korem, Anne-Catrin Uhlemann, Julian A Abrams.

Clinical and translational gastroenterology 11 (12), e00235 (2020)

​

Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome

Ruben AT Mars, Yi Yang, Tonya Ward, Mo Houtti, Sambhawa Priya, Heather R. Lekatz, Xiaojia Tang, Zhifu Sun, Krishna R Kalari, Tal Korem, Yogesh Bhattarai, Tenghao Zheng, Noam Bar, Gary Frost, Abigail J Johnson, Will van Treuren, Shuo Han, Tamas Ordog, Madhusudan Grover, Justin Sonnenburg, Mauro D’Amato, Michael Camilleri, Eran Elinav, Eran Segal, Ran Blekhman, Gianrico Farrugia, Jonathan R Swann, Dan Knights, Purna C Kashyap.

Cell 182 (6), 1460-1473 (2020)

​

The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View

Joao B Xavier, Vincent B Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T Pearson, Paul Macklin, Amir Mitchell, Ilya Shmulevich, Lei Xie, J Gregory Caporaso, Keith A Crandall, Nicole L Simone, Filipa Godoy-Vitorino, Timothy J Griffin, Katrine L Whiteson, Heather H Gustafson, Daniel J Slade, Thomas M Schmidt, Marina RS Walther-Antonio, Tal Korem, Bobbie-Jo M Webb-Robertson, Mark P Styczynski, W Evan Johnson, Christian Jobin, Jason M Ridlon, Andrew Y Koh, Michael Yu, Libusha Kelly, Jennifer A Wargo.

Trends in Cancer 6 (3), 192-204 (2020)

​

Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT

Jotham Suez*, Niv Zmora*, Gili Zilberman-Schapira*, Uria Mor*, Mally Dori-Bachash, Stavros Bashiardes, Maya Zur, Dana Regev-Lehavi, Rotem Ben-Zeev Brik, Sara Federici, Max Horn, Yotam Cohen, Andreas E Moor, David Zeevi, Tal Korem, Eran Kotler, Alon Harmelin, Shalev Itzkovitz, Nitsan Maharshak, Oren Shibolet, Meirav Pevsner-Fischer, Hagit Shapiro, Itai Sharon, Zamir Halpern, Eran Segal, Eran Elinav. 

Cell 174 (6), 1406-1423 (2018)

​

Environment dominates over host genetics in shaping human gut microbiota

Daphna Rothschild*, Omer Weissbrod*, Elad Barkan*, Alexander Kurilshikov, Tal Korem, David Zeevi, Paul I Costea, Anastasia Godneva, Iris N Kalka, Noam Bar, Smadar Shilo, Dar Lador, Arnau Vich Vila, Niv Zmora, Meirav Pevsner-Fischer, David Israeli, Noa Kosower, Gal Malka, Bat Chen Wolf, Tali Avnit-Sagi, Maya Lotan-Pompan, Adina Weinberger, Zamir Halpern, Shai Carmi, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Elinav, Eran Segal. 

Nature 555, 210-215 (2018)

​

Bread affects clinical parameters and induces gut microbiome-associated personal glycemic responses

Tal Korem*, David Zeevi*, Niv Zmora, Omer Weissbrod, Noam Bar, Maya Lotan-Pompan, Tali Avnit-Sagi, Noa Kosower, Gal Malka, Michal Rein, Jotham Suez, Ben Z Goldberg, Adina Weinberger, Avraham A Levy, Eran Elinav, Eran Segal. 

Cell Metabolism 25 (6), 1243-1253 (2017)

Covered widely, including: Cover image for Cell Metabolism, The Guardian, Newsweek, The Atlantic, CNN

​

Involvement of a gut-retina axis in protection against dietary glycemia-induced age-related macular degeneration

Sheldon Rowan, Shuhong Jiang*, Tal Korem*, Jedrzej Szymanski*, Min-Lee Chang, Jason Szelog, Christa Cassalman, Kalavathi Dasuri, Christina McGuire, Ryoji Nagai, Xue-Liang Du, Michael Brownlee, Naila Rabbani, Paul J Thornalley, James D Baleja, Amy A Deik, Kerry A Pierce, Justin M Scott, Clary B Clish, Donald E Smith, Adina Weinberger, Tali Avnit-Sagi, Maya Lotan-Pompan, Eran Segal, Allen Taylor. 

Proceedings of the National Academy of Sciences, 114 (22) E4472-E4481 (2017)

​

Talking about cross-talk: the immune system and the microbiome

David Zeevi*, Tal Korem*, Eran Segal.

Genome Biology 17 (1), 50 (2016) [Meeting report]

​

Taking it personally: personalized utilization of the human microbiome in health and disease

Niv Zmora*, David Zeevi*, Tal Korem*, Eran Segal, Eran Elinav.

Cell host & microbe 19 (1), 12-20 (2016)

​

Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling

Maayan Levy*, Christoph A Thaiss*, David Zeevi, Lenka Dohnalova, Gili Zilberman-Schapira, Jemal Ali Mahdi, Eyal David, Alon Savidor, Tal Korem, Yonatan Herzig, Meirav Pevsner-Fischer, Hagit Shapiro, Anette Christ, Alon Harmelin, Zamir Halpern, Eicke Latz, Richard A Flavell, Ido Amit, Eran Segal, Eran Elinav.

Cell 163 (6), 1248-1443 (2015)

​

Non-caloric artificial sweeteners and the microbiome: findings and challenges

Jotham Suez*, Tal Korem*, Gili Zilberman-Schapira*, Eran Segal, Eran Elinav.

Gut microbes 6 (2), 149-155 (2015)

​

Artificial sweeteners induce glucose intolerance by altering the gut microbiota

Jotham Suez, Tal Korem*, David Zeevi*, Gili Zilberman-Schapira*, Christoph A Thaiss, Ori Maza, David Israeli, Niv Zmora, Shlomit Gilad, Adina Weinberger, Yael Kuperman, Alon Harmelin, Ilana Kolodkin-Gal, Hagit Shapiro, Zamir Halpern, Eran Segal, Eran Elinav.

Nature 514, 181-186 (2014) 

Covered widely, including: Nature, The Economist, NY Times, Newsweek, Wall Street Journal, Washington Post

​

Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis

Christoph A Thaiss, David Zeevi, Maayan Levy, Gili Zilberman-Schapira, Jotham Suez, Anouk C Tengeler, Lior Abramson, Meirav N Katz, Tal Korem, Niv Zmora, Yael Kuperman, Inbal Biton, Shlomit Gilad, Alon Harmelin, Hagit Shapiro, Zamir Halpern, Eran Segal, Eran Elinav.

Cell 159 (3), 514-529 (2014)