Microbial Metagenomics Division

What we do

We collaborate and provide services in microbial ecology using metabarcoding and metagenomics tools. Our location near the Dead Sea is a front row sit to extreme habitats and their microbial communities, including humans and their microbiomes.

Hire Our Services

Metagenomics is a high throughput approach to understand the biological function of a pool of organisms in a sample. We can analyse your sample and predict the biological community and its biological functions in high resolution. We can test the change in the function and taxonomy following treatment or change in conditions. Find out more here.

Our laboratory is proficient in DNA metabarcoding and metagenomics techniques. We are experienced with many sample types including soil, water, or tissue from a range of organisms, and can conduct complex bioinformatic analyses. We can assist all stages of research starting with the experimental design, through data production and analysis, and ending with publication grade figures and data archiving. More information in the services page.

R & D Projects

The Acacia tree is very unique, 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. Continuing the work of Michael Brandwein, Dr. Shiri Meshner and Prof. Zvi Bentwitch, Dr. Amir Szitenberg studies 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, Prof. Emmilia Hodak from the Department of Dermatology, Rabin Medical Center, and Prof. Zvulunov from The Department of Dermatology, Soroka 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.

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.

Who We Are

Dr. Amir Szitenberg

Evolutionary biologist

Google Scholar

Twitter: @ASzitenberg


Dr. Ashraf Al Ashhab

Microbial ecologist

Google Scholar

linkedin: Ashraf Al Ashhab


Rivka Alexander Shani MSc

Lab Manager


Dr. Timur Yergaliyev

Post doctoral scientist


Yosef Avrahami MSc

Bioinformatician and research assitant


Danit Paker

Master's Student



Avigail Israel

Clinical research associate & Lab technician


Hana Dimeretz

Lab technician


Michael Brandwein

PhD Candidate

Cutaneous Microbiologist

Google Scholar, LinkedIn


Prof. Zvi Bentwich

Scientific Director,

Dead Sea Branch




The interaction of Dead Sea climatotherapy response with the skin microbial dynamics. Michael Brandwein's PhD project, now published in Photochemistry and Photobiology. A collaborative effort with Hebrew U, Open U, Rabin Medical Center and the DMZ-Dead Sea Clinic.


It was an honor and a pleasure to discuss microbiomes in general and skin microbiomes in particular, at the Intl. Fed. of Soc. of Cosmetic Chemists EMCEP seminar in Plovdiv Bulgaria, hosted and organised by the Bulgarian Association of Cosmetologists and the Department of Chemical & Pharmaceutical Engineering, Faculty of Chemistry & Pharmacy in Sofia University.


The preprint revealing ancient bear yeasts has now been accepted in mBio. We're happy to have been able to contribute to this project with the Ronen Hazan group (HUJI) and many others.


The preprint looking at eDNA of fish in England's largest lake, Lake Windermere, with Lori J Lawson Handley from the Unversity of Hull, et al., is now published in Environmental DNA, an exciting new open access journal.


After much deliberations (two years worth), we have acquired our very own Illumina iSeq100 sequencer and are being instructed regarding its usage by the Danyel Biotech staff, illumina's local representative.


We're delighted to be a part of the G-BIKE cost action, CA18134 - Genomic Biodiversity Knowledge for Resilient Ecosystems, harnessing the power of genomics to improve nature conservation. Here is me preaching G-BIKE to a bunch of sodomites (i.e. scientists working in the Sodom region) and international visitors, in the second international Dead Sea Summit, held by Tel Aviv University and the Dead Sea Research Institute at Masada.


We're happy to have been able to contribute to the Ronen Hazan group (HUJI) project, about ancient bear yeasts (read preprint)


A new paper just published assessing the effect of ancient Roman terraces on the on-site (on-field) geo-ecosystem functioning including soil microbial abundance.



The slides for my talk about the dynamics of microbial communities associated with root knot nematodes, delivered in the Europiean Scoiety of Nematology meeting in Ghent.


Delivering an oral presentation on the dynamics of microbial communities associated with root knot nematodes, and contributing to Dave Lunt's talk on sexual and asexual genomes in Meloidogyne, in the Europiean Scoiety of Nematology meeting in Ghent, Begium (find Waldo)


Another preprint showing the interaction of different human activities and land use on the freshwater microbiome. This study was conducted in Germany with collaborators from Haifa University and ADSSC


A new preprint abount eDNA of fish in England's largest lake, Lake Windermere, with Lori J Lawson Handley from the Unversity of Hull, et al.


A new paper is published investigating the soil restoration in heavily compacted arid land after a single tillage effect. A new insight into the microbiome abundance and soil physics following different tillage depths Stavi et., al 2018


Now hiring! See our lab technician opening.


Extract your own DNA in less than 5 min. Carrying out experiments with kids, where each one extracted their own DNA from their saliva using soap and table salt with some Vodka!


Pi Day! The science fair at DSASC Dead Sea. In a natural selection demo with beans, kids kept picking the ones less contrasting with the background rice colour. Could Darwin have been wrong?!


By the new year, a new article is published showing the significant effect of Dead Sea climatotherapy on human skin microbiome. the result shows that dramatic changes accrue in mycobiome variations, highlighting the importance of Malassezia spp. Read more


Congratulations to Michael on publishing a review paper in Frontiers in Immunology on antimicrobial peptides of the skin


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 describing 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

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