publications | Korem Lab

Selected publications (scholar)

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data

George I. Austin, Heekuk Park, Yoli Meydan, Dwayne Seeram, Tanya Sezin, Yue Clare Lou, Brian A. Firek, Michael J. Morowitz, Jillian F. Banfield, Angela M. Christiano, Itsik Pe’er, Anne-Catrin Uhlemann, Liat Shenhav†, Tal Korem†.

Nature Biotechnology 41, 1820-1828 (2023)

Coverage: Nature Reviews Microbiology highlight

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

William F. Kindschuh*, Federico Baldini*, Martin C. Liu*, Jingqiu Liao, Yoli Meydan, Harry H. Lee, Almut Heinken, Ines Thiele, Christoph A. Thaiss, Maayan Levy†, Tal Korem†.

Nature Microbiology 8, 246–259 (2023).

A reference map of potential determinants for the human serum metabolome

Noam Bar*, Tal Korem*, Omer Weissbrod, David Zeevi, Daphna Rothschild, Sigal Leviatan, Noa Kosower, Maya Lotan-Pompan, Adina Weinberger, Caroline I. Le Roy, Cristina Menni, Alessia Visconti, Mario Falchi, Tim D. Spector, The IMI DIRECT consortium, Jerzy Adamski, Paul W. Franks, Oluf Pedersen, Eran Segal.

Nature 588, 135-140 (2020)

Coverage: Nature News & Views

Structural variation in the gut microbiome associates with host health

David Zeevi*, Tal Korem*, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal.

Nature 568, 43-48 (2019)

Coverage: Nature Reviews Genetics highlight, Nature Microbiology News & View, Molecular Cell spotlight

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

Personalized nutrition by prediction of glycemic responses

David Zeevi*, Tal Korem*, Niv Zmora*, David Israeli*, Daphna Rothschild, Adina Weinberger, Orly Ben-Yacov, Dar Lador, Tali Avnit-Sagi, Maya Lotan-Pompan, Jotham Suez, Jemal Ali Mahdi, Elad Matot, Gal Malka, Noa Kosower, Michal Rein, Gili Zilberman-Schapira, Lenka Dohnalová, Meirav Pevsner-Fischer, Rony Bikovsky, Zamir Halpern, Eran Elinav, Eran Segal.

Cell 163 (5), 1079-1094 (2015)

Covered widely, including: Cover image for Cell, Video abstract, Nature, Time Magazine, NY Times, BBC, The Atlantic, Reddit AMA Series

Preprints

Distributional bias compromises leave-one-out cross-validation

George I Austin, Itsik Pe'er, Tal Korem†.

arXiv (2024)

Domain adaptation in small-scale and heterogeneous biological datasets

Seyedmehdi Orouji, Martin C Liu, Tal Korem†, Megan AK Peters†.

arXiv (2024) [Review]

Metagenomic coverage bias at transcription start sites is correlated with gene expression

Gordon Qian, Izaak Coleman, Tal Korem†, Joshua WK Ho†.

bioRxiv (2024)

Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models

George I Austin, Aya Brown Kav, Heekuk Park, Jana Biermann, Anne-Catrin Uhlemann, Tal Korem†.

bioRxiv (2024)

Compositional transformations can reasonably introduce phenotype-associated values into sparse features

George I Austin, Tal Korem†.

bioRxiv (2024)

Additional publications

Planning and analyzing a low-biomass microbiome study: A data analysis perspective
George I. Austin, Tal Korem†.

The Journal of Infectious Diseases (2024) [Review]

Robustness of cancer microbiome signals over a broad range of methodological variation

Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight†.

Oncogene 43 (15): 1127-48 (2024)

The salivary microbiome and predicted metabolite production are associated with Barrett's esophagus and high grade dysplasia or adenocarcinoma

Quinn S Solfisburg, Federico Baldini, Brittany L Baldwin-Hunter, George I. Austin, Harry H Lee, Heekuk Park, Daniel E Freedberg, Charles J Lightdale, Tal Korem†, Julian A Abrams†.

Cancer Epidemiology, Biomarkers & Prevention 33 (3): 371-80 (2023)

Microdiversity of the vaginal microbiome is associated with preterm birth

Jingqiu Liao*†, Liat Shenhav*, Julia A. Urban, Myrna Serrano, Bin Zhu, Gergory A. Buck, Tal Korem†.

Nature Communications 14: 4997 (2023)

pymgpipe: microbiome metabolic modeling in Python

Yoli Meydan*, Federico Baldini*, Tal Korem†.

Journal of Open Source Software, 8(88): 5545 (2023)

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)

Microbiota diurnal rhythmicity programs host transcriptome oscillations

Christoph A Thaiss*, Maayan Levy*, Tal Korem*, Lenka Dohnalová, Hagit Shapiro, Diego A Jaitin, Eyal David, Deborah R Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav.

Cell 167 (6), 1495-1510 (2016)

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)

Microsynteny is a powerful front for microbial strain tracking
Peiwen Cai, Tal Korem†.

Cell Reports Medicine 4 (9): 100862 (2024) [Spotlight]