Discovering microbiome-based disease risk factors

Publications

Cross-reactive antibodies against human coronaviruses and the animal coronavirome suggest diagnostics for future zoonotic spillovers

Author(s): Shelley Klompus, Sigal Leviatan, Thomas Vogl, Roei D. Mazor, Iris N. Kalka, Liat Stoler-Barak, Nachum Nathan, Ayelet Peres, Lihee Moss, Anastasia Godneva, Sharon Kagan Ben Tikva, Eilat Shinar, Hadas Cohen-Dvashi, Ronen Gabizon, Nir London, Ron Diskin, Gur Yaari, Adina Weinberger, Ziv Shulman, Eran Segal
Published in: Science Immunology, Issue 6/61, 2021, ISSN 2470-9468
Publisher: Science
DOI: 10.1126/sciimmunol.abe9950

Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota

Author(s): Thomas Vogl, Shelley Klompus, Sigal Leviatan, Iris N. Kalka, Adina Weinberger, Cisca Wijmenga, Jingyuan Fu, Alexandra Zhernakova, Rinse K. Weersma, Eran Segal
Published in: Nature Medicine, Issue 27/8, 2021, Page(s) 1442-1450, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01409-3

Structural variation in the gut microbiome associates with host health

Author(s): David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal
Published in: Nature, Issue 568/7750, 2019, Page(s) 43-48, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1065-y

A reference map of potential determinants for the human serum metabolome

Author(s): 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, Jerzy Adamski, Paul W. Franks, Oluf Pedersen, Eran Segal
Published in: Nature, Issue 588/7836, 2020, Page(s) 135-140, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2896-2

The road ahead in genetics and genomics

Author(s): Amy L. McGuire, Stacey Gabriel, Sarah A. Tishkoff, Ambroise Wonkam, Aravinda Chakravarti, Eileen E. M. Furlong, Barbara Treutlein, Alexander Meissner, Howard Y. Chang, Núria López-Bigas, Eran Segal, Jin-Soo Kim
Published in: Nature Reviews Genetics, Issue 21/10, 2020, Page(s) 581-596, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-020-0272-6

Large-scale association analyses identify host factors influencing human gut microbiome composition

Author(s): Alexander Kurilshikov, Carolina Medina-Gomez, Rodrigo Bacigalupe, Djawad Radjabzadeh, Jun Wang, Ayse Demirkan, Caroline I. Le Roy, Juan Antonio Raygoza Garay, Casey T. Finnicum, Xingrong Liu, Daria V. Zhernakova, Marc Jan Bonder, Tue H. Hansen, Fabian Frost, Malte C. Rühlemann, Williams Turpin, Jee-Young Moon, Han-Na Kim, Kreete Lüll, Elad Barkan, Shiraz A. Shah, Myriam Fornage, Joanna Szopinska
Published in: Nature Genetics, Issue 53/2, 2021, Page(s) 156-165, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-020-00763-1

Wearable and digital devices to monitor and treat metabolic diseases.

Author(s): Keshet A, Reicher L, Bar N, Segal E.
Published in: Nature Metabolism, 2023, ISSN 2522-5812
Publisher: Springer
DOI: 10.1038/s42255-023-00778-y

The rationale and design of the personal diet study, a randomized clinical trial evaluating a personalized approach to weight loss in individuals with pre-diabetes and early-stage type 2 diabetes

Author(s): Collin J. Popp, David E. St-Jules, Lu Hu, Lisa Ganguzza, Paige Illiano, Margaret Curran, Huilin Li, Antoinette Schoenthaler, Michael Bergman, Ann Marie Schmidt, Eran Segal, Anastasia Godneva, Mary Ann Sevick
Published in: Contemporary Clinical Trials, Issue 79, 2019, Page(s) 80-88, ISSN 1551-7144
Publisher: Elsevier BV
DOI: 10.1016/j.cct.2019.03.001

Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes.

Author(s): Ben-Yacov O, Godneva A, Rein M, Shilo S, Lotan-Pompan M, Weinberger A, Segal E.
Published in: Gut, 2023, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2022-329201

Effect of a Personalized Diet to Reduce Postprandial Glycemic Response vs a Low-fat Diet on Weight Loss in Adults With Abnormal Glucose Metabolism and Obesity: A Randomized Clinical Trial

Author(s): Popp CJ, Hu L, Kharmats AY, Curran M, Berube L, Wang C, Pompeii ML, Illiano P, St-Jules DE, Mottern M, Li H, Williams N, Schoenthaler A, Segal E, Godneva A, Thomas D, Bergman M, Schmidt AM, Sevick MA
Published in: JAMA Network Open, 2022, ISSN 2574-3805
Publisher: American Medical Association
DOI: 10.1001/jamanetworkopen.2022.33760

Antibody signatures in inflammatory bowel disease: current developments and future applications

Author(s): Bourgonje AR, Vogl T, Segal E, Weersma RK
Published in: Trends Molecular Medicine, 2022, ISSN 1471-4914
Publisher: Elsevier BV
DOI: 10.1016/j.molmed.2022.05.004

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

Author(s): Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S; Lifelines Cohort Study; Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A
Published in: Immunity, 2023, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2023.04.003

SARS-CoV-2 antibody testing for estimating COVID-19 prevalence in the population

Author(s): Thomas Vogl, Sigal Leviatan, Eran Segal
Published in: Cell Reports Medicine, Issue 2/2, 2021, Page(s) 100191, ISSN 2666-3791
Publisher: Cell
DOI: 10.1016/j.xcrm.2021.100191

Prediction of Personal Glycemic Responses to Food for Individuals With Type 1 Diabetes Through Integration of Clinical and Microbial Data

Author(s): Shilo S, Godneva A, Rachmiel M, Korem T, Kolobkov D, Karady T, Bar N, Wolf BC, Glantz-Gashai Y, Cohen M, Zuckerman Levin N, Shehadeh N, Gruber N, Levran N, Koren S, Weinberger A, Pinhas-Hamiel O, E. Segal.
Published in: Diabetes Care, 2021, ISSN 0149-5992
Publisher: American Diabetes Association
DOI: 10.2337/dc21-1048

Clinically Accurate Prediction of Glucose Levels in Patients with Type 1 Diabetes

Author(s): Yotam Amar, Smadar Shilo, Tal Oron, Eran Amar, Moshe Phillip, Eran Segal
Published in: Diabetes Technology & Therapeutics, Issue 22/8, 2020, Page(s) 562-569, ISSN 1520-9156
Publisher: Mary Ann Liebert Inc.
DOI: 10.1089/dia.2019.0435

Structured elements drive extensive circular RNA translation

Author(s): CK. Chen, R. Cheng, J. Demeter, J. Chen, S. Weingarten-Gabbay, L. Jiang, MP. Snyder, JS. Weissman, E. Segal, PK. Jackson, HY. Chang.
Published in: Molecular Cell, 2021, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2021.07.042

Impact of dietary interventions on pre-diabetic oral and gut microbiome, metabolites and cytokines

Author(s): Shoer S, Shilo S, Godneva A, Ben-Yacov O, Rein M, Wolf BC, Lotan-Pompan M, Bar N, Weiss EI, Houri-Haddad Y, Pilpel Y, Weinberger A, Segal E.
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-41042-x

Prediction of gestational diabetes based on nationwide electronic health records

Author(s): Nitzan Shalom Artzi, Smadar Shilo, Eran Hadar, Hagai Rossman, Shiri Barbash-Hazan, Avi Ben-Haroush, Ran D. Balicer, Becca Feldman, Arnon Wiznitzer, Eran Segal
Published in: Nature Medicine, Issue 26/1, 2020, Page(s) 71-76, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-019-0724-8

Axes of a revolution: challenges and promises of big data in healthcare

Author(s): Smadar Shilo, Hagai Rossman, Eran Segal
Published in: Nature Medicine, Issue 26/1, 2020, Page(s) 29-38, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-019-0727-5

The pros, cons, and many unknowns of probiotics

Author(s): Jotham Suez, Niv Zmora, Eran Segal, Eran Elinav
Published in: Nature Medicine, Issue 25/5, 2019, Page(s) 716-729, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-019-0439-x

The Gut Microbiome and Individual-Specific Responses to Diet

Author(s): Avner Leshem, Eran Segal, Eran Elinav
Published in: mSystems, Issue 5/5, 2020, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00665-20

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

Author(s): Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Se
Published in: Nature, 2023, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-05546-8

Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease

Author(s): Talmor-Barkan Y, Bar N, Shaul AA, Shahaf N, Godneva A, Bussi Y, Lotan-Pompan M, Weinberger A, Shechter A, Chezar-Azerrad C, Arow Z, Hammer Y, Chechi K, Forslund SK, Fromentin S, Dumas ME, Ehrlich SD, Pedersen O, Kornowski R, E. Segal.
Published in: Nature Medicine, 2022, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-01686-6

Potential roles of gut microbiome and metabolites in modulating ALS in mice

Author(s): Eran Blacher, Stavros Bashiardes, Hagit Shapiro, Daphna Rothschild, Uria Mor, Mally Dori-Bachash, Christian Kleimeyer, Claudia Moresi, Yotam Harnik, Maya Zur, Michal Zabari, Rotem Ben-Zeev Brik, Denise Kviatcovsky, Niv Zmora, Yotam Cohen, Noam Bar, Izhak Levi, Nira Amar, Tevie Mehlman, Alexander Brandis, Inbal Biton, Yael Kuperman, Michael Tsoory, Leenor Alfahel, Alon Harmelin, Michal Schwartz, Ad
Published in: Nature, Issue 572/7770, 2019, Page(s) 474-480, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1443-5

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species

Author(s): Leviatan S, Shoer S, Rothschild D, Gorodetski M, Segal E.
Published in: Nature Communication, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31502-1

Prediction of type 2 diabetes mellitus onset using logistic regression-based scorecards

Author(s): Edlitz Y, Segal E
Published in: Elife, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.71862

Rich data sets could end costly drug discovery

Author(s): Eran Segal
Published in: Nature, Issue 577/7792, 2020, Page(s) S19-S19, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/d41586-020-00200-7

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients

Author(s): Vogl T, Kalka IN, Klompus S, Leviatan S, Weinberger A, Segal E
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abq2422

Microbiome and metabolome features of the cardiometabolic disease spectrum

Author(s): Fromentin S, Forslund SK, Chechi K, Aron-Wisnewsky J, Chakaroun R, Nielsen T, Tremaroli V, Ji B, Prifti E, Myridakis A, Chilloux J, Andrikopoulos P, Fan Y, Olanipekun MT, Alves R, Adiouch S, Bar N, Talmor-Barkan Y, Belda E, Caesar R, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Le Chatelier E, Julienne H, Olsson L, Pedersen HK, Pons N, Quinquis B, Rouault C, Ro
Published in: Nature Medicine, 2022, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-01688-4

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome

Author(s): Ruben A.T. 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. S
Published in: Cell, Issue 182/6, 2020, Page(s) 1460-1473.e17, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2020.08.007

Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals

Author(s): Leviatan S, Vogl T, Klompus S, Kalka IN, Weinberger A, Segal E.
Published in: Immunity, 2022, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2022.11.004

Effects of personalized diets by prediction of glycemic responses on glycemic control and metabolic health in newly diagnosed T2DM: a randomized dietary intervention pilot trial

Author(s): Rein M, Ben-Yacov O, Godneva A, Shilo S, Zmora N, Kolobkov D, Cohen-Dolev N, Wolf BC, Kosower N, Lotan-Pompan M, Weinberger A, Halpern Z, Zelber-Sagi S, Elinav E, E. Segal
Published in: BMC Medicine, 2022, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-022-02254-y

Potential role of indolelactate and butyrate in multiple sclerosis revealed by integrated microbiome-metabolome analysis

Author(s): Izhak Levi, Michael Gurevich, Gal Perlman, David Magalashvili, Shay Menascu, Noam Bar, Anastasia Godneva, Liron Zahavi, Danyel Chermon, Noa Kosower, Bat Chen Wolf, Gal Malka, Maya Lotan-Pompan, Adina Weinberger, Erez Yirmiya, Daphna Rothschild, Sigal Leviatan, Avishag Tsur, Maria Didkin, Sapir Dreyer, Hen Eizikovitz, Yamit Titngi, Sue Mayost, Polina Sonis, Mark Dolev, Yael Stern, Anat Achiron, Era
Published in: Cell Reports Medicine, Issue 2/4, 2021, Page(s) 100246, ISSN 2666-3791
Publisher: Elsevier B.V.
DOI: 10.1016/j.xcrm.2021.100246

Identifying gut microbes that affect human health

Author(s): Sigal Leviatan, Eran Segal
Published in: Nature, Issue 587/7834, 2020, Page(s) 373-374, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/d41586-020-03069-8

CGMap: Characterizing continuous glucose monitor data in thousands of non-diabetic individuals

Author(s): Keshet A, Shilo S, Godneva A, Talmor-Barkan Y, Aviv Y, Segal E, Rossman H
Published in: Cell Metabolism, 2023, ISSN 1550-4131
Publisher: Cell Press
DOI: 10.1016/j.cmet.2023.04.002

BREAst Cancer Personalised NuTrition (BREACPNT): dietary intervention in breast cancer survivors treated with endocrine therapy - a protocol for a randomised clinical trial

Author(s): Rein MS, Dadiani M, Godneva A, Bakalenik-Gavry M, Morzaev-Sulzbach D, Vachnish Y, Kolobkov D, Lotan-Pompan M, Weinberger A, Segal E, Gal-Yam EN.
Published in: BMJ Open, 2022, ISSN 2044-6055
Publisher: BMJ Publishing Group
DOI: 10.1136/bmjopen-2022-062498

The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control

Author(s): Shilo S, Godneva A, Rachmiel M, Korem T, Bussi Y, Kolobkov D, Karady T, Bar N, Wolf BC, Glantz-Gashai Y, Cohen M, Levin NZ, Shehadeh N, Gruber N, Levran N, Koren S, Weinberger A, Pinhas-Hamiel O, E. Segal.
Published in: Diabetes Care, 2022, ISSN 0149-5992
Publisher: American Diabetes Association
DOI: 10.2337/dc21-1656

BIPS-A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library

Author(s): Leviatan S, Kalka IN, Vogl T, Klompas S, Weinberger A, Segal E.
Published in: PLoS Computational Biology, 2022, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1010663

The human tumor microbiome is composed of tumor type–specific intracellular bacteria

Author(s): Deborah Nejman, Ilana Livyatan, Garold Fuks, Nancy Gavert, Yaara Zwang, Leore T. Geller, Aviva Rotter-Maskowitz, Roi Weiser, Giuseppe Mallel, Elinor Gigi, Arnon Meltser, Gavin M. Douglas, Iris Kamer, Vancheswaran Gopalakrishnan, Tali Dadosh, Smadar Levin-Zaidman, Sofia Avnet, Tehila Atlan, Zachary A. Cooper, Reetakshi Arora, Alexandria P. Cogdill, Md Abdul Wadud Khan, Gabriel Ologun, Yuval Bussi,
Published in: Science, Issue 368/6494, 2020, Page(s) 973-980, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aay9189

The gut microbiome: a key player in the complexity of amyotrophic lateral sclerosis (ALS)

Author(s): Sarah L. Boddy, Ilaria Giovannelli, Matilde Sassani, Johnathan Cooper-Knock, Michael P. Snyder, Eran Segal, Eran Elinav, Lynne A. Barker, Pamela J. Shaw, Christopher J. McDermott
Published in: BMC Medicine, Issue 19/1, 2021, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-020-01885-3

Clinical efficacy of fecal microbial transplantationtreatment in adults with moderate‐to‐severe atopicdermatitis

Author(s): Mashiah J, Karady T, Fliss-Isakov N, Sprecher E, Slodownik D, Artzi O, Samuelov L, Ellenbogen E, Godneva A, E. Segal, Maharshak N.
Published in: Immunology Inflammation and Disease, 2021, ISSN 2050-4527
Publisher: Wiley
DOI: 10.1002/iid3.570

Reporting guidelines for human microbiome research: the STORMS checklist

Author(s): Mirzayi C, Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elin
Published in: Nature Medicine, 2021, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01552-x

An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents

Author(s): Rothschild D, Leviatan S, Hanemann A, Cohen Y, Weissbrod O, Segal E.
Published in: PLoS One, 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0265756

A Significant Expansion of Our Understanding of the Composition of the Human Microbiome

Author(s): Sigal Leviatan, Eran Segal
Published in: mSystems, Issue 4/1, 2019, Page(s) e00010-19, ISSN 2379-5077
Publisher: American Society of Microbiology
DOI: 10.1128/msystems.00010-19

Recording bacterial responses to changes in the gut environment

Author(s): Zahavi L, Segal E
Published in: Science, 2022, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abq1455

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