Microbiome-human interactions Laboratory – Prof. Nitsan Maharshak >>

Microbiome-Human Interactions Laboratory


Our Vision

Our lab focuses on the role of enteric bacteria in disease conditions in humans and in-vitro cell culture models. Specifically, we study how bacterial proteases impact the epithelial barrier function and how enteric microbial alterations are related to diseases.
Clinically, investigate inflammatory bowel diseases and perform interventional studies such as diets, fecal microbial transfer and physical activity on these diseases. Additionally, we examine clinical, dietary, microbial and laboratory factors for prognostication of disease exacerbation and response to therapy


Contact Us

Primary Investigators

Prof. Nitsan Maharshak - Lab PI

Head of IBD unit, Gastro. Dept.;Internal Medicine Department
Phone: +972-3-6947305
Email: nitsanm@tlvmc.gov.il


Dr. Lael Werner - Lab Manager

Phone: +972-36947632
Email: laelw@tlvmc.gov.il


Sourasky building

Research Center for Digestive Tract & Liver Diseases Sourasky Medical Center,‎
6 Weizmann St. 64239. Tel Aviv.



The interactions between bacterial proteases and the epithelial barrier function.

We study how dysbiosis and bacterial dependent proteolytic activity are involved in epithelial barrier dysfunction and IBD exacerbations. Fecal microbiome from patients with active/non-active IBD is analyzed and is cultured with Caco2 cells monolayers. Receptors and molecular pathways that are associated with tight junction disruption are studied.

Fecal auto-transplantation for enteric microbial rehabilitation post Helicobacter pylori therapy

Current guidelines mandate H pylori eradication with 2-3 antibiotics for 14 days. Worldwide prevalence of H pylori is estimated at 30-80% of all populations. Thus, an enormous number of people are receiving and will receive this regimen. This may result in multiple side effects and in eradication of important bacterial species to human health, exposing humans to multiple disease conditions. In this project, we aim to test whether Auto-transplantation of preserved fecal microbiome (collected prior to antibiotics exposure) after H pylori eradication, restores the healthy enteric microbiome and prevents multiple unwanted dysbiosis related symptoms and disease conditions.

The impact of perioperative nutrition for Crohn’s disease patients.

This project examines efficacy of exclusive enteral nutrition (EEN) in peri-operative CD patients. We hypothesize that malnourished CD patients receiving EEN prior to surgery, and during the 4 weeks post-operation, will improve in clinical outcomes and post-operative complication rate will decline, in comparison to CD patients receiving high protein diet without EEN.

Special physical exercises as a therapeutic intervention for IBD.

The positive effects of physical activity can be achieved by modifying factors such as sleep quality, bowel circadian rhythm, and perceived stress; as well as impact the enteric microbiome. The aim of this pilot study is to examine whether daily routine, self-exercise of special physical exercises sets, designed exclusively for IBD patients, can improve patients’ quality of life and clinical disease activity. Special physical exercise sets, designed by a highly experienced yoga teacher include explicit drills inspired by yoga poses, postulated to improve ‘abdominal health’. Videos are performed at home for 30 consecutive days.

Antibody biomarker discovery in IBD patients using a novel high throughput assay

We will leverage a novel high throughput assay to identify the antibody reactivities against 344,000 antigens in 500 IBD patients and compare them to their fecal microbiome profiles. We will be able to mine for novel IBD biomarkers at unprecedented depth in various clinical set-ups: predictors of flare ups and response to various biological therapies. This project is carried out as a collaboration with Prof. Eran Segal, at the Weizmann Institute of Science.


Our Team

Current Staff

Head of research


Basic Science Project

Past Staff

Current funding


Highlight Publications

 Use of Fecal transplantation with a novel diet for mild to moderate active ulcerative colitis: The CRAFT UC randomized controlled trial.

Sarbagili Shabat C, Scaldaferri F, Zittan E, Hirsch A, Chiara Mentella M, Musca T, Cohen NA, Ron Y, Fliss Isakov N, Pfeffer J, Yaakov M, Fanali C, Turchini L, Masucci L, Quaranta G, Kolonimos N, Godneva A, Weinberger A, Kopylov U, Levine A, Maharshak N.

J Crohn’s Colitis 2022. 16(3):369-378.

Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis.

Mashiah J, Karady T, Fliss-Isakov N, Sprecher E, Slodownik D, Artzi O, Samuelov L, Ellenbogen E, Godneva A, Segal E, Maharshak N.

Immun Inflamm Dis. 2022 10(3):e570.


Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation

Federici S, Kredo-Russo S, Valdés-Mas R, Kviatcovsky D, Weinstock E, Matiuhin Y, Silberberg Y, Atarashi K, Furuichi M, Oka A, Liu B, Fibelman M, Weiner IN, Khabra E, Cullin N, Ben-Yishai N, Inbar D, Ben-David H, Nicenboim J, Kowalsman N, Lieb W, Kario E, Cohen T, Geffen YF, Zelcbuch L, Cohen A, Rappo U, Gahali-Sass I, Golembo M, Lev V, Dori-Bachash M, Shapiro H, Moresi C, Cuevas-Sierra A, Mohapatra G, Kern L, Zheng D, Nobs SP, Suez J, Stettner N, Harmelin A, Zak N, Puttagunta S, Bassan M, Honda K, Sokol H, Bang C, Franke A, Schramm C, Maharshak N, Sartor RB, Sorek R, Elinav E.

Cell. 2022 185(16):2879-2898.e24.

More Publications >>

The Effect of the Crohn’s Disease Exclusion Diet on Patients with Pouch Inflammation: An Interventional Pilot Study.

Isakov NF, Kornblum J, Zemel M, Cohen NA, Hirsch A, Maharshak N.

Clin Gastroenterol Hepatol. 2022:S1542-3565(22)00398-6.

Higher Maintenance Adalimumab Trough Levels are Associated With Achievement of Advanced Remission Targets in Patients With Inflammatory Bowel Disease

Ritter E, Hirsch A, Naomi Fliss Isakov N, Ron Y, Cohen NA,  Maharshak N.J Clin Gastroenterol. 2021.  55 (9), 810-814

Vedolizumab is effective and safe in elderly inflammatory bowel disease patients: a binational, multicenter, retrospective cohort study Cohen NA, Plevris N, Kopylov U, Grinman A, Ungar B, Yanai H, Leibovitzh H, Fliss Isakov N, Hirsch A, Ritter E, Ron Y, Bar-Gil Shitrit A, Goldin E, Dotan I, Ben Horin S, Lees W, Maharshak N.

United European Gastroenterol J. 2020.

Fruit consumption is associated with alterations in microbial composition and lower rates of pouchitis

Godny L*, Maharshak N*, Reshef L, Goren I, Yahav L, Fliss-Isakov N, Gophna U, Tulchinsky H, Dotan I. *Equal Contribution.

J Crohn’s Colitis. 2019;13(10):1265-72.

The Crohn’s disease exclusion diet for induction and maintenance of remission in adults with mild-to-moderate Crohn’s disease (CDED-AD): an open-label, pilot, randomised trial Yanai H, Levine A, Hirsch A, Sigall Boneh R, Kopylov U, Banai Eran H, Cohen NA, Ron Y, Goren I, Leibovitzh H, Wardi J, Zittan E, Ziv-Baran T, Abramas, L, Fliss-Isakov N, Raykhel B, Pfeffer Gik T, Dotan I, Maharshak N.

Lancet Gastroenterol and Hepatol. 2021; 7(1),49-59

Faecal proteases from pouchitis patients activate protease activating receptor-2 to disrupt the epithelial barrier

Hoffman S, Aviv Cohen N, Carroll IM, Tulchinsky H, Borovok I, Dotan I, Maharshak N.

    J Crohn’s Colitis. 2019;13(12):1558-68.

Less Publications >>

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

 Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E.

Cell. 2018;174(6):1406-1423.e16.

Alterations of enteric microbiota in patients with a normal ileal pouch are predictive of pouchitis

Maharshak N, Cohen NA, Reshef L, Tulchinsky H, Gophna U, Dotan I.

     J Crohn’s Colitis. 2017;11(3):314-20.


From The Press