Scientific papers:


Youngster I, Eshel A, Geva M, Danylesko I, Henig I, Zuckerman T, Fried S, Yerushalmi R, Shem-Tov N, Fein JA, Bomze D, Shimoni A, Koren O, Shouval R, and  Nagler A. Fecal Microbiota Transplantation in Capsules for the Treatment of Steroid Refractory and Steroid Dependent Acute Graft vs. Host Disease: A Pilot Study. Bone Marrow Transplant. Online ahead of print. 

Frishman S, Nuriel-Ohayon M, Turjeman S, Pinto Y, Yariv O, Tenenbaum-Gavish K, Peled Y, Poran E, Pardo J, Chen R, Muller E, Borenstein E, Hod M, Louzoun Y, Schwartz B, Hadar E, Collado MC, Koren O. Positive Effects of Diet-Induced Microbiome Modification on GDM In Mice Following Human Faecal Transfer. Gut. Online ahead of print.

Carmel J, Ghanayem N, Mayouf R, Saleev N, Chaterjee I, Getselter D, Tikhonov E, Turjeman S, Shaalan M, Khateeb S, Kuzminsky A, Kvetniy-Ferdman N, Kronos T, Bretler-Zager T, Koren O, and Elliott E. Bacteroides is Increased in an Autism Cohort and Induces Autism-Relevant Behavioral Changes in Mice in a Sex-Dependent Manner. NPJ Biofilms Microbiomes. 9(1):103.

Koren O, Konnikova L, Brodin P, Mysorekar IU, and Collado MC. The Maternal Gut Microbiome in Pregnancy: Implications for the Developing Immune System. Nat Rev Gastroenterol Hepatol. (1):35-45.


Kuzi S, Zgairy S, Byrne BA, Suchodolski J, Turjeman SC, Park SY, Aroch I, Hong M, Koren O, and Lavy E. Giardiasis and Diarrhea in Dogs: Does the Microbiome Matter? J Vet Intern Med. Online ahead of print. 

Kamer O, Rinott E, Tsaban G, Kaplan A, Yaskolka Meir A, Zelicha H, Knights D, Tuohy K, Fava F, Uwe Scholz M, Ziv O, Rubin E, Bluher M, Stumvoll M, Ceglarek U, Clement K, Koren O, Hu FB, Stampfer MJ, Wang DD, Youngster I, and Shai I. Successful Weight Regain Attenuation by Autologous Fecal Microbiota Transplantation is Associated with Non-Core Gut Microbiota Changes During Weight Loss; Randomized Controlled Trial. Gut Microbes. 15(2):2264457.

Suissa R, Olender T, Malitsky S, Golani O, Turjeman S, Koren O, Meijler MM, and Kolodkin-Gal I. Metabolic Inputs in the Probiotic Bacterium Lacticaseibacillus rhamnosus Contribute to Cell-Wall Remodeling and Increased Fitness. NPJ Biofilms Microbiomes. 9(1):71. 

 Tzemah-Shahar R, Turjeman S, Sharon E, Gamliel G, Hochner H, Koren O, and Agmon M. Signs of aging in Midlife: Physical Function and Sex Differences in Microbiota. Geroscience. Online ahead of print. 

Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, Mor H, Koren O, and Louzoun Y. Recipient-Independent, High-Accuracy FMT-Response Prediction and Optimization in Mice and Humans. Microbiome.

Diaz Heijtz R, Keane L, and Koren O. Early-Life Sensitive Periods for Antibiotic-Induced Shifts In Neuro-Immune Developmental Trajectories and Vulnerability to Brain Disorders. Brain Behav Immun. 114:78-79.

Turjeman S, Sharon E, Levin R, Oralewska B, Szaflarska-Poplawska A, Bierla JB, Cukrowska B, and Koren O. Celiac-The Lone Horse? An Autoimmune Condition Without Signals of Microbiota Dysbiosis. Microbiol Spectr. 11(5):e0146323.

Shtossel O, Isakov H, Turjeman S, Koren O, and Louzoun Y. Ordering Taxa in Image Convolution Networks Improves Microbiome-Based Machine Learning Accuracy. Gut Microbes. 15(1):2224474.

Fontaine F, Turjeman S, Callens K, and Koren O. The Intersection of Undernutrition, Microbiome, and Child Development in the First Years of Life. Nature Communications. 14(1):1-9.

Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cardenas P, Baldeon ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, and Taroncher-Oldenburg G. Multi-Level Analysis of the Gut–Brain Axis Shows Autism Spectrum Disorder-Associated Molecular and Microbial Profiles. Nature Neuroscience. 26(7):1208-1217.

Avizemel O, Frishman S, Pinto Y, Michael Y, Turjeman S, Tenenbaum-Gavish K, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Schwartz B, Hadar E, Koren O, and Agay-Shay K. Residential greenness, gestational diabetes mellitus (GDM) and microbiome diversity during pregnancy. International Journal of Hygiene and Environmental Health. 1(251): 114191.

Manghi P, Blanco-Míguez A, Manara S, NabiNejad A, Cumbo F, Beghini F, Armanini F, Golzato D, Huang KD, Thomas AM, Piccinno G., Puncochar M, Zolfo M, Lesker TR, Bredon M, Planchais J, Glodt J, Valles-Colomer M, Koren O, Pasolli E, Asnicar F, Strowig T, Sokol H, and Segata N. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Reports. 42(5): 112464.

Malka O, Malishev R, Bersudsky M, Rajendran M, Krishnamohan M, Shaik J, Chamovitz DA, Tikhonov E, Sultan E, Koren O, Apte RN, Rosental B, Voronov E, and Jelinek R. Tryptophol acetate and tyrosol acetate, small molecule metabolites identified in a probiotic mixture, inhibit hyperinflammation. Journal of Innate Immunity. 15 (1): 531–547.

Weiner A, Turjeman S, and Koren O. Gut microbes and host behavior: The forgotten members of the gut-microbiome. Neuropharmacology. 3:109453.

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, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, and Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 613(7945): 639-649.

Pinto Y, Frishman S, Turjeman S, Eshel A, Nuriel-Ohayon M, Shrossel O, Ziv O, Walters W, Parsonnet J, Ley C, Johnson EL, Kumar K, Schweitzer R, Khatib S, Magzal F, Muller E, Tamir S, Tenenbaum-Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Borenstein E, Ley RE, Schwartz B, Louzoun Y, Hadar E, and Koren O. Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. Gut. 72(5): 918-928.



Suissa R, Oved R, Maan H, Hadad U, Gilhar O, Meijler MM, Koren O, and Kolodkin-Gal I. Context-Dependent Differences in the Functional Responses of Lactobacillaceae Strains to Fermentable Sugars. Frontiers in Microbiology. 24(13): 949932.

Gilboa A, Hope R, Ben Simon S, Polak P, Koren O, and Yaari G. Ontogeny of the B Cell Receptor Repertoire and Microbiome in Mice. The Journal of Immunology. 208(12): 2713-25.

Feldman R, Yirmiya K, Turjeman S, Shtossel O, Zagoory-Sharon O, Moadi L, Louzoun Y, and Koren O. Microbiome Mediates Development of PTSD and Resilience. Research Square. preprint.

Cheng J, Kolba N, Sisser P, Turjeman S, Even C, Koren O, and Tako E. Intraamniotic Administration (Gallus gallus) of Genistein Alters Mineral Transport, Intestinal Morphology, and Gut Microbiota. Nutrients.14(17): 3473.

Grinberg M, Levin R, Neuman H, Ziv O, Turjeman S, Gamliel G, Nosenko R, and Koren O. Antibiotics Increase Aggression Behavior and Aggression-Related Pheromones and Receptors in Drosophila melanogaster. Iscience. 25(6): 104371.

Rinott E, Meir AY, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Scholz MU, Koren O, Stampfer MJ, and Wang DD. The Effects of the Green-Mediterranean Diet on Cardiometabolic Health are Linked to Gut Microbiome Modifications: A Randomized Controlled Trial. Genome Medicine. 14(1): 1-5.

Glinert A, Turjeman S, Elliott E, and Koren O. Microbes, Metabolites and (Synaptic) Malleability, Oh My! The Effect of the Microbiome on Synaptic Plasticity. Biological Reviews of the Cambridge Philosophical Society. 97(2): 582-599.

Suissa R, Oved R, Jankelowitz G, Turjeman S, Koren O, and Kolodkin-Gal, I. Molecular Genetics for Probiotic Engineering: Dissecting Lactic Acid Bacteria. Trends in Microbiology. 30(3): 293-306.
Eshel A, Sharon I, Nagler A, Bomze D, Danylesko I, Fein JA, Geva M, Henig I, Shimoni A, Zuckerman T, Youngster I, Koren O , and Shouval R. Origins of Bloodstream Infections Following Fecal Microbiota Transplantation: A Strain-Level Analysis. Blood Advances. 6(2): 568–573.

Agarwal N,  Kolba N, Khen N, Even C, Turjeman S, Koren O, and Tako, E. Quinoa Soluble Fiber and Quercetin Alter the Composition of the Gut Microbiome and Improve Brush Border Membrane Functionality and Morphology In Vivo (Gallus gallus). Nutrients. 14(3): 448.

Turjeman S and Koren O. Using the Microbiome in Clinical Practice. Microbial Biotechnology. 5(1):129-134. 


Kennedy KM. et al. Over-Celling Fetal Microbial Exposure. Cell. 184(24):5839-41.

Hiltunen H, Hanani H, Luoto R, Turjeman S, Ziv O, Isolauri E, Salminen S, Koren O, and Rautava S. Preterm Infant Meconium Microbiota Transplant Induces Growth Failure, Inflammatory Activation, and Metabolic Disturbances in Germ-Free Mice. Cell Reports Medicine. 2(11):100447.

Mirzayi C. et al. Reporting Guidelines for Human Microbiome Research: The STORMS Checklist. Nature Medicine. 27: 1885-1892.

Jasner Y, Belogolovski A, Ben-Itzhak M, Koren O, and Louzoun Y. Microbiome Preprocessing Machine Learning Pipeline. Frontiers in Immunology. 2021;12.

Turjeman S and Koren O. ARGuing the Case for (or Against) Probiotics. Trends in Microbiology. 29(11): 959-960

Gomes MJC, Kolba N, Agarwal N, Kim D, Eshel A, Koren O, and Tako, E., 2021. Modifications in the Intestinal Functionality, Morphology and Microbiome Following Intra-Amniotic Administration (Gallus gallus) of Grape (Vitis vinifera) Stilbenes (Resveratrol and Pterostilbene). Nutrients. 13(9), p.3247.

Lichtenstein M, Turjerman S, Pinto JM, Barash O, and Koren O. Pathophysiology of SARS-CoV-2 Infection in the Upper Respiratory Tract and Its Relation to Breath Volatile Organic Compounds. mSystems. 6(4):e00104-21.

Tal S, Tikhonov E, Aroch I, Hefetz L, Turjeman S,  Koren O, and Kuzi S. Developmental Intestinal Microbiome Alterations in Canine Fading Puppy Syndrome: A Prospective Observational Study. npj Biofilms Microbiomes. 7(52).

Ben Izhak M, Eshel A, Cohen R, Madar-Shapiro L, Meiri H, Wachtel C, Leung C, Messick E, Jongkam N, Mavor E, Sapozhnikov S, Maharshak N, Abu-Abeid S, Alis A, Mahler I, Meoded A, Eldar SM, Koren O, and Louzoun Y. Projection of Gut Microbiome Pre- and Post-Bariatric Surgery To Predict Surgery OutcomemSystems. 6(3):e01367-20.

Lassi M, Tomar A , Comas-Armangué G, Vogtmann R, Dijkstra DJ, Corujo D, Gerlini R, Darr J, Scheid F, Rozman J, Aguilar-Pimentel A, Koren O, Buschbeck M, Fuchs H, Marschall S, Gailus-Durner V, Hrabe de Angelis M, Plösch T, Gellhaus A, and Teperino R. Disruption of Paternal Circadian Rhythm Affects Metabolic Health in Male Offspring via Nongerm Cell Factors. Science Advances. 7(22):eabg6424.
Rinott E, Youngster I, Meir AY, Tsaban G, Kaplan A, Zelicha H, Rubin E, Koren O, and Shai I. Autologous Fecal Microbiota Transplantation Can Retain the Metabolic Achievements of Dietary Interventions. European Journal of Internal Medicine. 92:17-23.
Turjeman S, Collado MC, and Koren O. The Gut Microbiome in Pregnancy and Pregnancy Complications. Current Opinion in Endocrine and Metabolic Research. 18:133-138.
Binyamin D, Nitzan O, Azrad M, Hamo Z, Koren O, and Peretz A. The Microbial Diversity Following Antibiotic Treatment of Clostridioides difficile Infection. BMC Gastroenterology. 21(1):1-6.
Agranyoni O, Meninger-Mordechay S, Uzan A, Ziv O, Salmon-Divon M, Rodin D, Raz O, Koman I, Koren O, Pinhasov A, and Navon-Venezia S. Gut Microbiota Determines the Social Behavior of Mice and Induces Metabolic and Inflammatory Changes in Their Adipose Tissue. npj Biofilms and Microbiomes7(1):1-14.
Uzan-Yulzari A, Turta O, Belogolovski A, Ziv O, Kunz C, Perschbacher S, Neuman H, Pasolli E, Oz A, Ben-Amram H, Kumar H, Ollila H, Kaljonen A, Isolauri E, Salminen S,  Lagtrom H, Segata N, Sharon I, Louzoun Y, Ensenauer R, Rautava S, and Koren O. Neonatal Antibiotic Exposure Impairs Child Growth During the First Six Years of Life by Perturbing Intestinal Microbial Colonization. Nature Communications. 26;12(1):1-2.


Rohana H, Azrad M, Nitzan O, Adler A, Binyamin D, Koren O, and Peretz A. Characterization of Clostridioides difficile Strains, the Disease Severity, and the Microbial Changes They Induce. Journal of Clinical Medicine. 9(12):4099.
Baruch EN, Youngster I, Ben-Betzalel G, Ortenberg R, Lahat A, Katz L, Adler K, Dick-Necula D, Raskin S, Bloch N, Rotin D, Anafi L, Avivi C, Melnichenko J, Steinberg-Silman Y, Mamtani R, Harati H, Asher N, Shapira-Frommer R, Brosh-Nissimov T, Eshet Y, Ben-Simon S, Ziv O, Khan MAW, Amit M, Ajami NJ, Barshack I, Schachter J, Wargo JA, Koren O, Markel G, and Boursi B. Fecal Microbiota Transplant Promotes Response in Immunotherapy-Refractory Melanoma Patients. Science. 371(6529):602-9.
Uzan-Yulzari A, Morr M, Tareef-Nabwani H, Ziv O, Magid-Neriya D, Armoni R, Muller E, Leibovici A, Borenstein E, Louzoun Y, Shai A, and Koren O. The Intestinal Microbiome, Weight, and Metabolic Changes in Women Treated by Adjuvant Chemotherapy for Breast and Gynecological Malignancies. BMC Med. 18(1):1-0.
Goldberg MR, Mor H, Neriya DM, Magzal F, Muller E, Appel MY, Nachshon L, Borenstein E, Tamir S, Louzoun Y, Youngster I, Elizur A, and Koren O. Microbial Signature in IgE-Mediated Food Allergies. Genome Med. 12(1):1-8.
Binyamin D, Werbner N, Nuriel-Ohayon M, Uzan A, Mor H, Abbas A, Ziv O, Teperino R, Gutman R, and Koren O. The Aging Mouse Microbiome Has Obesogenic Characteristics. Genome Med. 12;12(1):87. 
Grinberg M, Neuman H, Ziv O, Turjeman S, Nosenko R, and Koren O. Antibiotics Increase Aggression Behavior and Aggression-Related Pheromones and Receptors in Drosophila melanogaster. bioRxiv. preprint.
Carboni J, Reed S, Kolba N, Eshel A, Koren O, and Tako E, Alterations in the Intestinal Morphology, Gut Microbiota, and Trace Mineral Status Following Intra-Amniotic Administration (Gallus gallus) of Teff (Eragrostis tef) Seed Extracts. Nutrients. 12:3020.
Li Y, Toothaker JM, Ben-Simon S, Ozeri L, Schweitzer R, McCourt BT, McCourt CC, Werner L, Snapper SB, Shouval DS, Khatib S, Koren O, Agnihorti S, Tseng G, and Konnikova L. In Utero Human Intestine Harbors Unique Metabolomic Features Including Bacterial Metabolites. JCI Insight. 5;5(21):e138751.

Lapidot L, Amir A, Ben-Simon S, Veitsman E, Ezra OC, Davidov Y, Weiss P, Bradichevski T, Segev S, Koren O, and Safran M. Alterations of the Salivary and Fecal Microbiome in Patients with Primary Sclerosing CholangitisHepatol Int. 1(70):1152A.

Tenenbaum-Gavish K, Sharhabi-Nov A, Binyamin D, Møller HJ, Danon D, Rothman L, Hadar E, Idelson A, Vogel I, Koren O, Nicolaides KH, Gronbaek H, and Meiri H. First Trimester Biomarkers for prediction of Gestational Diabetes Mellitus. Placenta. 101:80-89.

Rinott E, Youngster I, Meir AY, Tsaban G, Zelicha H, Kaplan A, Knights D, Tuohy K, Fava F, Scholz MU, Ziv O, Reuven E, Tirosh A, Rudich A, Blüher M, Stumvoll M, Ceglarek U, Clement K, Koren O, Wang DD, Hu FB, Stampfer MJ, and Shai I. Effects of Diet-Modulated Autologous Fecal Microbiota Transplantation on Weight Regain. Gastroenterology. S0016-5085(20)35111-8.

Shouval R, Eshel A, Dubovski B, Kuperman AA, Danylesko I, Fein JA, Fried S, Geva M, Kouniavski E, Neuman H, Armon-Omer A,  Shahien R, Muller E, Noecker C, Borenstein E, Louzoun Y, Nagler A, and Koren O. Patterns of Salivary Microbiota Injury and Oral Mucositis in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation. Blood Adv. 4(13):2912-2917.

Lapidot Y, Amir A, Nosenko R, Uzan-Yulzari A, Veitsman E, Cohen-Ezra O, Davidov Y, Weiss P, Bradichevski T, Segev S, Koren O, Safran M, Ben-Ari Z. Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular CarcinomamSystems. 00153-20.

Frankiensztajn LM, Elliott E, Koren O. The microbiota and the hypothalamus-pituitary-adrenocortical (HPA) axis, implications for anxiety and stress disordersCurr Opin Neurobiol. 62:76-82.

Kayyal M, Javkar T,  Firoz Mian M, Binyamin D, Koren O, McVey Neufeld KA, and Forsythe P. Sex Dependent Effects of Post-Natal Penicillin on Brain, Behavior and Immune Regulation Are Prevented by Concurrent Probiotic Treatment. Sci Rep. 10(1):10318.

Beasley JT, Johnson AAT, Kolba N, Bonneau JP, Glahn RP, Ozeri L, Koren O, and Tako,E. Nicotianamine-chelated Iron Positively Affects Iron Status, Intestinal Morphology and Microbial Populations in Vivo (Gallus gallus). Sci Rep. 10(1):2297.

Shahar RT, Koren O, Matarasso S, Shochat T, Magzal F, and Agmon M. Attributes of Physical Activity and Gut Microbiome in Adults: A Systematic Review. Int J Sports Med. 10.1055/a-1157-9257.

Champagne-Jorgensen K, Firoz Mian M, Kay S, Hanani H, Ziv O, McVey Neufeld KA, Koren O, and Bienenstock J. Prenatal Low-Dose Penicillin Results in Long-Term Sex-Specific Changes to Murine Behaviour, Immune Regulation, and Gut Microbiota. Brain Behav Immun. 84:154-163.


Janzon A, Goodrich JK, Koren O, TEDDY Study Group, Waters JL, and Ley RE. Interactions Between the Gut Microbiome and Mucosal Immunoglobulins A, M, and G in the Developing Infant Gut. mSystems. 26;4(6).

van der Giessen J*, Binyamin D*, Belogolovski A, Frishman S, Tenenbaum-Gavish K, Hadar E, Louzoun Y, Peppelenbosch MP, van der Woude CJ, Koren O*, and Fuhler GM*. Modulation of Cytokine Patterns and Microbiome During Pregnancy in IBD. Gut. 69(3):473-486. *These authors contributed equally.

Calatayud M, Koren O, and Collado MC. Maternal Microbiome and Metabolic Health Program Microbiome Development and Health of the Offspring. Trends Endocrinol Metab. 30(10):735-744.

Lukić I, Getselter D, Koren O, and Elliott E. Role of Tryptophan in Microbiota-Induced Depressive-Like Behavior: Evidence From Tryptophan Depletion Study. Front Behav Neurosci.13:123.

Shapiro J, Cohen NA, Shalev V, Uzan A, Koren O, and Maharshak N. Psoriatic Patients have a Distinct Structural and Functional Fecal Microbiota Compared with Controls. J Dermatol. 46(7):595-603.

Bretler T, Weisberg H, Koren O, and Neuman H. The Effects of Antipsychotic Medications on Microbiome and Weight gain in Children and Adolescents.  BMC Med. 17(1):112.

Werbner M, Barsheshet Y, Werbner N, Zigdon M, Averbuch I, Ziv O, Brant B, Elliott E, Gelberg S, Titelbaum M, Koren O, and Avni O. Social-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper Cells. mSystems. 4(4). pii: e00292-18.

Nuriel-Ohayon M, Neuman H, Ziv O, Belogolovski A, Barsheshet Y, Bloch N, Uzan A, Lahav R, Peretz A, Frishman S, Hod M, Hadar E, Louzoun Y, Avni O, and Koren O. Progesterone Increases Bifidobacterium Relative Abundance during Late PregnancyCell Rep. 27(3):730-736.e3.

Stehlikova Z, Kostovcik M, Kostovcikova K, Kverka M, Juzlova K, Rob F, Hercogova J, Bohac P, Pinto Y, Uzan A, Koren O, Tlaskalova-Hogenova H, and Jiraskova Zakostelska Z. Dysbiosis of Skin Microbiota in Psoriatic Patients: Co-occurrence of Fungal and Bacterial Communities. Front Microbiol10:438.

Lukić I, Getselter D, Ziv O, Oron O, Reuveni E, Koren O, and Elliott E. Antidepressants Affect Gut Microbiota and Ruminococcus flavefaciens is Able to Abolish Their Effects on Depressive-Like Behavior. Transl Psychiatry. 9(1):133.

Neuman H, Mor H, Bashi T, Givol O, Watad A, Shemer A, Volkov A, Barshack I, Fridkin M, Blank M, Shoenfeld Y, and Koren O. Helminth-Based Product and the Microbiome of Mice with LupusmSystems. 4(1).


Dias DM, Kolba N, Binyamin D, Ziv O, Regini Nutti M, Martino HSD, Glahn RP, Koren O, and Tako E. Iron Biofortified Carioca Bean (Phaseolus vulgaris L.)-Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota in Vivo (Gallus gallus).  Nutrients. 10(12) pii: E1970.

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Duranti S, Lugli GA, Mancabelli L, Turroni F, Ferrario C, Milani C, Mangifesta M, Anzalone R, Viappiani A, Yassour M, Vlamakis H, Xavier R, Collado CM, Koren O, Tateo S, Soffiati M, Pedrotti A, Ventura M, Huttenhower C, Bork P, and Segata N. Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. Cell Host Microbe. 24(1):133-145.

Neuman H, Forsythe P, Uzan A, Avni O* and Koren O*. Antibiotics in Early Life: Dysbiosis and the Damage Done. FEMS Microbiol Rev. 42(4): 489-499. *These authors contributed equally.

Reed S, Knez M, Uzan A, Stangoulis JCR, Glahn RP, Koren O, and Tako E. Alterations in the Gut (Gallus gallus) Microbiota Following the Consumption of Zinc Biofortified Wheat (Triticum aestivum)-Based Diet. J Agric Food Chem. 66(25): 6291-6299.

Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, del Rio TG, Tringe SG, Buckler ES, Dangl JL, and Ley RE. Large-Scale Replicated Field Study of Maize Rhizosphere Identifies Heritable Microbes. PNAS. 115(28): 7368-7373.

Binyamin D, Nitzan O, Azrad M, Hamo Z, Koren O*, and Peretz A*. In vitro Activity of Tedizolid, Dalbavancin, and Ceftobiprole Against Clostridium difficile. Front Microbiol. 9:1256. *These authors contributed equally.

Tabouy L, Getselter D, Ziv O, Karpuj M, Tabouy T, Lukic I, Maayouf R, Werbner N, Ben-Amram H, Nuriel-Ohayon Meital, Koren O, and Evan E. Dysbiosis of Microbiome and Probiotic Treatment in a Genetic Model of Autism Spectrum DisordersBrain Behav Immun. 2018;73:310-319.

Nunberg M*, Werbner N*, Neuman H, Bersudsky M, Braiman A, Ben-Shoshan M, Ben Izhak M, Louzoun Y, Apte RN, Voronov E, and Koren O. IL-1α Deficient Mice Have an Altered Gut Microbiota Leading to Protection from DSS-Induced Colitis. mSystems3:e00213-17. *These authors contributed equally. Editor’s Choice and Cover Image.

Avni O* and Koren O*. Molecular (Me)micryCell Host Microbe. 23(5):576-578. *These authors contributed equally.

Gerassy-Vainberg S, Blatt A, Danin-Poleg Y, Gershovich K, Sabo E, Nevelsky A, Daniel S, Dahan A, Ziv O, Dheer R, Abreu MT, Koren O, Kashi Y, and Chowers Y. Radiation Induces Proinflammatory Dysbiosis: Transmission of Inflammatory Susceptibility by Host Cytokine Induction. Gut. 67(1):97-107.


Dahan S, Segal Y, Watad A, Azrielant S, Shemer A, Maymon D, Stroev YI, Sobolevskaya PA, Korneva EA, Blank M, Gilburd B, Shovman O, Amital H, Ehrenfeld M, Tanay A, Kivity S, Pras E, Chapman J, Damoiseaux J, Cervera R, Putterman C, Shapiro I, Mouthon L, Periconne R, Bizzaro N, Koren O, Riemekasten G, Chereshnev VA, Mazurov VI, Goloviznin M, Gurevich V, Churilov LP, and  Shoenfeld Y. Novelties in the Field of Autoimmunity – 1st Saint Petersburg Congress of Autoimmunity, the Bridge Between East and West. Autoimmun Rev. 16(12):1175-1184.

Reed S, Neuman H, Glahn RP, Koren O, and Tako E. Characterizing the Gut (Gallus gallus) Microbiota Following the Consumption of an Iron Biofortified Rwandan Cream Seeded Carioca (Phaseolus Vulgaris L.) Bean-Based Diet. PLoS One. 12(8): e0182431.

Ben-Amram H, Bashi T, Werbner N, Neuman H, Fridkin M, Blank M, Shoenfeld Y, and Koren O. Tuftsin-Phosphorylcholine Maintains Normal Gut Microbiota in Collagen Induced Arthritic Mice.  Front Microbiol. 8:1222.

Pitlik S and Koren O. How holobionts get sick: towards a unifying scheme of disease. Microbiome, 5:64.

Neuman H & O Koren. The Gut Microbiota: A Possible Factor Influencing Systemic Lupus ErythematosusCurr Opin Rheumatol. 29(4): 374-377.

Leclercq S, Mian FM, Stanisz AM, Bindels LB, Cambier E, Ben-Amram H, Koren O, Forsythe P, and Bienenstock J. Low-Dose Penicillin in Early Life Induces Long-Term Changes in Murine Gut Microbiota, Brain Cytokines and Behavior. Nat Commun. 8:15062.

Neuman H & Koren O. The Pregnancy Microbiome. Nestle Nutrition Institute Workshop Series. 88:1-9.


Nuriel-Ohayon M, Neuman H & O Koren. Microbial Changes During Pregnancy, Birth and Infancy. Front Microbiol. 7:1031.

Shamriz O, Mizrahi H, Werbner M, Shoenfeld Y, Avni O*, and Koren O*. The Microbiota at the Crossroads of AutoimmunityAutoimmun Rev. 15(9):859-869. *These authors contributed equally.

Kuperman A and O Koren. Antibiotics During Pregnancy: How Bad is It? BMC Med. 14(1): 91.


Reed S, Neuman H, Moscovich S, Glahn RP, Koren O, and Tako E. Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function. Nutrients. 7(12): 9768-84.

Neuman H,  Debelius JW, Knight R and Koren O. Microbial Endocrinology: The Interplay Between Microbiota and the Endocrine SystemFEMS Microbiol Rev. 39(4): 509-521.

Kuperman A and Koren O. Editorial: The Era of Fecal Microbiota Transplantation. Isr Med Assoc J. 17:2-3.

Chassing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE, and Gewirtz AT. Dietary Emulsifiers Alter Gut Microbiota-Intestinal Interactions Promoting Colitis and Metabolic Syndrome. Nature. 5(519): 92-96.

Tracy A, Koren O, Douglas N, Weil E, and Harvell D. Persistent Shifts in Caribbean Coral Microbiota are Linked to the 2010 Warm Thermal Anomaly. Environ Microbiol Rep. 7(3): 471-9.


Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, and Ley RE. Human Genetics Shape the Gut Microbiome. Cell. 150(4): 789-799. Recommended by Faculty of 1000.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, and Ley RE. Conducting a Microbiome Study. Cell. 158(2): 250-262.

Bel S, Elkis Y, Elifantz H, Koren O, Ben-Hamo R, Lerer-Goldshtein T, Rahimi R, Ben Horin S, Nyska A, Shpungin S, and Nir U. Reprogrammed and Transmissible Intestinal Microbiota Confer Diminished Susceptibility to Induced Colitis in TMF-/- Mice. PNAS. 111(13): 4964-9.

Chassing B, Koren O, Carvalho FA, Ley RE, and Gewirtz AT. AIEC Pathobiont Instigates Chronic Colitis in Susceptible Hosts by Altering Microbiota Composition. Gut. 63(7): 1069-80.


Di Rienzi SC*, Sharon I*, Wrighton KC, Koren O, Hug LA, Thomas BC, Goodrich JK, Bell JT, Spector TD, Banfield J*, and Ley RE*. The Human Gut and Groundwater Harbor Non-Photosynthetic Bacteria Belonging to a New Candidate Phylum Sibling to Cyanobacteria. eLIFE. 2:e01102. *These authors contributed equally. Recommended by Faculty of 1000.

Peiffer JA*, Spor A*, Jin Z, Koren O, Tringe SG, Dangl JL, Buckler ES, and Ley RE. Diversity and Heritability of the Maize Rhizosphere Microbiome Under Field Conditions. PNAS. 110(16): 6548-53. *These authors contributed equally.

Koren O*, Knights D*, Pena AG*, Waldron L, Segata N, Knight R, Huttenhower C, and Ley RE. A Guide to Enterotypes Across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. PLoS Comput Biol. 9(1), e1002863. *These authors contributed equally.


Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed H, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S, and Ley RE. Host Remodeling of the Gut Microbiome and Metabolic Changes During Pregnancy. Cell. 150(3), 470-480. Recommended by Faculty of 1000.

Carvalho FA, Koren O, Johansson M, Nalbantogl I, Aitken JD, SuY, Chassing B, Walters WA, Pena AG, Clemente JC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, and Gewirtz AT. Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice. Cell Host Microbe. 12(2), 139-152.

The Human Microbiome Consortium. Structure, Function and Diversity of the Healthy Human Microbiome.   Nature. 486, 207-214. Recommended by Faculty of 1000.

The Human Microbiome Consortium. A Framework for Human Microbiome Research. Nature. 486, 215-221.
Recommended by Faculty of 1000.

Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M, and Gewirtz AT. Interleukin-1β (IL-1β) Promotes Susceptibility of Toll-Like Receptor 5 (TLR5) Deficient Mice to Colitis. Gut. 61, 373-384.

Ravussin Y*, Koren O*, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, and Leibel R. Response of Gut Microbiotas to Diet Composition and Weight Loss in Lean and Obese Mice. Obesity. 20(4), 738-47. *These authors contributed equally.

Larsson E, Tremaroli V, Shiuan Lee Y, Koren O, Nookaew I, Fricker A, Nielsen J, Ley RE, and Backhed F. Analysis of Gut Microbial Regulation of Host Gene Expression Along the Length of the Gut and Regulation of Gut Microbial Ecology through MyD88. Gut. 61:1124-31. Recommended by Faculty of 1000.


Ran-Ressler R, Khailova L, Arganbright KM, Adkins-Rieck CK, Jouni ZE, Koren O, Ley RE, Brenna JT, and Dvorak B. Branched Chain Fatty Acids Alter Gastrointestinal Microbial Ecology and Reduce the Incidence of Necrotizing Enterocolitis in a Neonatal Rat Model. PLoS One. 6(12), e29032.

Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley RE, Wakeland EK, and Hooper LV. The Antibacterial Lectin RegIIIg Promotes the Spatial Segregation of Microbiota and Host in the Intestine. Science, 334, 255-58. Recommended by Faculty of 1000.

Werner JJ *, Koren O*, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, and Ley RE. Impact of Training Sets on Classification of High-Throughput Bacterial 16S rRNA Gene Surveys. ISME J. 6(1), 94-103. *These authors contributed equally.

Yilmaz, P, The MIMARKS Consortium. Minimum Information About a Aarker Gene Sequence (MIMARKS) and Minimum Information About Any (x) Sequence (MIxS) Specifications. Nat Biotechnol. 29, 415-20.

Spor A*, Koren O*, and Ley RE. Unraveling the Effects of the Environment and Host Genotype on the Gut Microbiome. Nat Rev Microbiol. 9, 279-90. *These authors contributed equally.

Koren O*, Spor A*, Felin J*, Fåk F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE, and Bäckhed F. Human Oral, Gut and Plaque Microbiota in Patients with Atherosclerosis. PNAS. 15:108 Suppl 1:4592-8. *These authors contributed equally. Recommended by Faculty of 1000.

Knights D, Kuczynski J, Koren O, Ley RE, Field D, Knight R, DeSantis TZ, and Kelley ST. Supervised Classification of Microbiota Mitigates Mislabeling ErrorsISME J. 5, 570-573.


Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, and Knight R. Direct Sequencing of the Human Microbiome Readily Reveals Community Differences. Genome Biol. 5, 210-219.

Koren O and Rosenberg E. Bacteria Associated with the Bleached and Cave Coral Oculina patagonica. Microb Ecol. 55, 523-529.

Rosenberg E, Koren O, Reshef L, Efrony R, and Zilber-Rosenberg I. The Role of Microorganisms in Coral Health, Disease and Evolution. Nat Rev Microbiol. 5, 355-362. Recommended by Faculty of 1000.

Reshef L, Koren O, Loya Y, Zilber-Rosenberg I, and  Rosenberg E. The Coral Probiotic Hypothesis.   Env Microbiol. 8, 2068-2073.

Koren O and Rosenberg E. Bacteria Associated with Mucus and Tissues of the Coral Oculina patagonica in Summer and Winter. Appl Environ Microbiol. 72, 5254- 5259. Recommended by Faculty of 1000.

Knezevich V, Koren O, Ron EZ, and Rosenberg E. Petroleum Bioremediation in Seawater Using Guano as the Fertilizer. Bioremediat J. 10, 83-91.

Koren O, Knezevich V, Ron EZ, and Rosenberg E. Petroleum Pollution Bioremediation Using Water-Insoluble Uric Acid as the Nitrogen Source. Appl Environ Microbiol. 69, 6337-6339.

Books & Chapters

Koren O and Rautava, S.  (2020) The Human Microbiome in Early Life: Implications to Health and Disease. Elsevier.

Collado MC and Koren O. (2019) Microbiome and Pregnancy Complications in New Technologies in Perinatal Medicine. Hod M, Berghella V, D’Alton M, Di Renzo GC, Gratacós E, and Fanos V (eds). CRC Press.

Neuman H and Koren O. (2015) The Gut Microbiome in Encyclopedia of Cell Biology. Bradshaw RA and Stahl PD (eds). Elsevier.

Koren O and Ley RE. (2015) The Human Intestinal Microbiota and Microbiome in Yamada’s Textbook of Gastroenterology, 6th Edition. Podolsky DK, Camilleri M, Fitz JG, Kalloo AN, Shanahan F, and Wang TC (eds). Wiley-Blackwell.

Rosenberg E and Koren O. (2006) Vibrios in Coral Health and Disease in The Biology of Vibrios. Thompson FL, Austin B, and Swings J (eds). ASM Press.

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