Microbial Metagenomics Division

What we do

We collaborate and provide services in the filed of microbial ecology and evolution using metabarcoding and metagenomics tools. Our location near the Dead Sea is a front row sit to extreme habitats and their microbial communities. We take an ecological approach towards the study of holobionts, in which all the aspects of an ecosystem are applicable to the host and its symbionts.

R & D Projects

Acacia is a unique tree, capable of existing where most trees do not. Dr. Ashraf Al Ashhab studies it's phylosphere bacteria to understand their contribution to the tree's high durability and to harness them for use in agriculture and cosmetics. This is done in collaboration with Dr. Gideon Winters from DSASC in Hatzeva.

The Dead Sea is a unique climatotherapy location. Michael Brandwein, Prof. Zvi Bentwitch, Dr. Amir Szitenberg and Dr. Joseph Meloul study the skin microbiome associated with a range of diseases, and the effect of climatotherapy on skin bacteria. This research is in collaboration with Dr. Marco Harari of the DMZ medical center and Prof. Emmilia Hodak from the Department of Dermatology, Rabin Medical Center

Root knot nematodes are a major crop pest throughout vast regions of the glob. They are known to interact with soil and plant bacteria to successfully infest plants. Dr. Amir Szitenberg is interested in the microbial soil and plant community associated with intense infestation and in ways to manipulate it in order to inhibit nematode infestation. We collaborate with Shimon Pivonia and Dr. Yael Bar Lavan from the Hatzeva R&D on this project, and with Prof. David Bird, from NC state University.

Fish are an extremely susceptible cultivar, with elaborate water treatment procedures usually in place. Dr Ashraf Al-Ashhab is interested in the effect of the commonly used UV treatment on the native bacterial community of fish skin, and the role of the skin community in fighting of infections. This research is a collaboration with Galit Sharon DVM, from ILOR in Eilat.

The Dead Sea basin is a unique source of biodiversity, given a range of extreme habitats. We characterize the unique microorganismal biodiversity in water bodies in the region.

Root Knot nematodes are a devastating crop parasite around the world. The Arava protected horticulture is also affected by this pest. Yet, genomic resources and microbiome information in this group is scares. Dr. Amir Szitenberg studies the genome evolution of Root Knot nematodes and their associated bacteria in order to understand their biology.

Hire Our Services

Our laboratory is self sufficient regarding workflows of DNA metabarcoding and metagenomics. We are capable of producing data from a range of biological samples, and conduct complex bioinformatics analyses. We can assist in any step starting with the experimental design, through data production and analysis, ending with publication grade figures and data archiving.

This flier has more information on our workflows.

Or you can contact Dr. Guy Cohen


Who We Are

Dr. Amir Szitenberg

Evolutionary biologist

Google Scholar

Twitter: @ASzitenberg


Dr. Ashraf Al Ashhab

Microbial ecologist

Google Scholar

linkedin: Ashraf Al Ashhab


Michael Brandwein

PhD Student

Cutaneous Microbiologist


Rivka Alexander Shani MSc

Lab Manager


Avigail Israel

Clinical research associate & Lab technician


Hana Dimeretz

Lab technician


Prof. Zvi Bentwich

DSASC Dead Sea branch head




A new paper Genome Biology and Evolution on the genome evolution of tropical apomictic root knot nematodes by Amir and collaborators, revealing an interesting mechanism for genetic diversification in the absence of meiosis.


The Dead Sea branch away day, together with DSASC management and administrative team, trying to break the shame barrier. September is almost cool enough to enjoy the outdoors.


Michael, Avigail and Ashraf have a new publication in Acta Dermato-Venereologica. Showing stability of the microbiome of healthy skin to the extreme climatic conditions in the Dead Sea.


Greetings to Dr. Ashraf Al Ashhab on his new publication at the journal of biofouling: Biofouling of reverse osmosis membranes: effects of cleaning on biofilm microbial communities, membrane performance, and adherence of extracellular polymeric substances. Biofouling:Vol. 33, No. 5,pp. 397-409. doi: 10.1080/08927014.2017.1318382


Our lab joined the ISM conference with three posters

Dr. Amir Szitenberg, Rivka Alexander Shani and Hana Dimeretz presenting a poster about the community variation in root knot nematode bacteria

Dr. Ashraf Al Ashhab presenting the Fish microbiome project

Michael Brandwein presenting a poster about the detection of cutaneous microorganisms by volatile metabolite signatures


Heavily compacted Arid soil restoration: sampling next to Sede Boker to investigate the effect of various tillage practices on soil restoration, with Dr. Ilan Stavi


Rivka Alexander Shani has a new paper about about the long term HIF-1α transcriptional activation and its essential role in heat-acclimation mediated cross-tolerance in Am J Physiol Regul Integr Comp Physiol.


We are finally starting to sample soil and root bacterial communities in nematode infested horticulture. Sampling is taking place in Hatzeva, with Shimon Pivonia


The MinION has arrived at the microbial metagenomics core facility. Looking forward to these nice long bacterial contigs!


We had a visit from gifted students from Shoam and the region. We discussed the importance of bacteria in the world and the delicate balance they are in. As a case study, we examined our own gut microbiome by playing the wonderful Gut Check game, created by David Coil, Erin Johnson and Prof. Jonathan Eisen, from UC Davis.


Congrats to Michael Brandwein on his first review publication, with supervisors Shiri Meshner (DSASC) and Doron Steinberg (HUJI)!

This is a review about microbial biofilms and the human skin microbiome in npj Biofilms and Microbiomes.


A new home for the ADSSC, Dead Sea Branch in Masada. The new building is designed to accommodate the needs of the Microbial Metagenomics Core Facility laboratory workflows, with dedicated environmental samples room, pre and post PCR rooms, bacterial culturing room and a sequencing suite.


A new paper for Amir, together with Dave Lunt (U of Hull), Mark Blaxter (U of Edinburgh), Soyeon Cha, Charlie Opperman and Dave Bird (NC state) about the stochastic nature of transposable elements in GBE