What We Do?
Our Research
Our main research interest is to understand the ecological and evolutionary forces that shape microbial communities in nature and specifically, in gut environments. Understanding these forces enables us to predict and modulate the composition of the microbiome towards optimized functionality.
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Whats new?
We explored plasmid dispersal across 3467 human gut microbiome samples worldwide. Our findings show neutral gene flow, but under pressure, key genes breach barriers. Join us in uncovering insights at Nature Communication !
We explored uncharted bacterial species in the human gut microbiota capable of degrading complex cellulosic polysaccharides, revealing their origins, adaptations to diverse host lifestyles and diets, and potential sources. Read more in Science.
We discover that a plasmid coded defense system serves as a gateway for prosperous mutualistic interactions that otherwise could become waring and distractive ones.Check out our new paper at nature microbiology .
- Check out this recent #BehindThePaper interview we conducted together with our collaborators from the Medalia Lab for #FEMSmicroBlog, discussing our recent work utilizing cryo-electron microscopy to gain new perspectives of microbial ecology and evolution
- In our recent work published in microLIFE we used cryo-electron microscopy to capture the specific microscopic structure of microbes. We were able to classify microbes by their structure and create an atlas of rumen bacterial and archaeal species, combining both complementary fields of structural biology and microbial ecology.
Check out the latest Cell Voices to read Itzik's perspective on what collective features of microbial communities our lab is aiming to unravel.
In this new paper published in the ISME Journal we find that the rumen metaproteome is remarkably plastic at the genome level & is predictive to microbiome & host feed efficiency states.
Check out our new paper published in the ISME Journal as part of a collaboration with the Elia Lab, where we study an Asgard archaeal protein family conserved across all domains of life.
Looking through the microbial lens - Our recent work published in eLife, where we use single-cell structural biology to understand the ecology of cellulose degradation at scales in which microbial life unfolds
Check out our new study published in the ISME journal, demonstrating how differences in gut microbial composition across lineages are translated into host-specific metabolomes, see the thread below from the main findings
Discover More
Microbial communities are everywhere and drive many basic processes in our everyday life, concerning agriculture, health and the environment. We study the evolutionary forces that act on microbial communities in nature, as well as the ecological forces that shape them. Specifically, we are interested in the factors that determine microbial community assembly in gut environments, as well as the effect of gene mobility via plasmids on their ecology.
For this purpose, we use state of the art tools, such as deep sequencing, big data analysis, metabolomics, fluorescence-activated cell sorting (FACS), high-performance microscopy and classical aerobic and anaerobic microbiology approaches. This knowledge is, in turn, used to understand and to influence the role of microbial communities in health and disease, as well as in agricultural systems. Hence, it is expected to have implications for future developments in food sustainability, renewable energy and medicine.
Read about our ongoing projects
- Community Ecology of The Microbiome
Community Ecology of The Microbiome
Our interests include community assembly dynamics of the microbiome in high temporal and genetic resolution. This enables us to identify the potential of alternative assemblages in gut communities, providing further information about basic ecological concepts. For example, a particular species may pre-condition future states of the community due to its ecological interactions, stimulating the growth of a specific subset of species and inhibiting others. We relate these variations in community composition to changes in ecological function, particularly the metabolic efficiency of the microbiome. - Evolutionary, Ecological and Structural Basis of Microbial Fiber Degradation in Nature
Evolutionary, Ecological and Structural Basis of Microbial Fiber Degradation in Nature
For as long as there has been life on land, Earth's terrestrial food chain has been based on the microbial degradation of cellulose-based fiber of photosynthetic products. Although extensive research has been dedicated to the evolutionary origins and mechanisms of the photosynthetic processes of land plants that generate fiber, very little is known about the evolution and ecology of microbial fiber breakdown. We colboarte with Prof. William F. Martin, Prof. Ohad Medalia, Prof. Edward A. Bayer and Prof. Dörte Becher in a focused effort uniting cutting-edge research tools and expertise, by applying microbial ecology, extracellular proteomics, fiber-degrading enzymology, structural biology and molecular evolution, to understand the evolutionary history of fiber degradation and its interconnectivity with microbial ecology at a nanoscale resolution. Achieving our goals will enable us to gain answers and deep insights into how ecology and evolution of microbial fiber degradation are intertwined and reflected at the single-microbe and community context, from the biochemical, structural and physiological perspectives. Our study will thus provide a stepping-stone towards defining and better understanding the central role of fiber degradation in nature and will reveal the Earth history of natural fiber-degrading microbial ecosystems. - The Rumen Microbiome
The Rumen Microbiome
Ruminants host a complex relationship with their residing ruminal microbiota; a relationship which has evolved for millions of years and impacts our everyday lives regarding food availability, environmental issues and economic concerns. The microbiome resides in the upper digestive tract of the animal in a chambered compartment named the rumen and is mainly responsible for most of the food's digestion and absorption. Therefore, understanding and characterizing this complex ecosystem is of major interest to us. Our results show that individual hosts vary greatly in the different pathways utilized by their microbiome for harvesting energy. Alternative pathways may conserve energy by maximizing energy production while suppressing methane emission- a quality termed 'feed efficiency'. These pathways rely on species composition and the metabolic functions they provide. We bring together microbial genomics, anaerobic microbiology and microbial community ecology to learn how cooperative or antagonistic ecological interactions between the microbial species that reside in the rumen control the establishment of alternative microbiomes with different functional efficiencies. - Plasmidome Dynamics Within The Microbiome
Plasmidome Dynamics Within The Microbiome
Gut microbial communities are extremely diverse, exceptionally dense and sustain an intricate relationship with their mammalian host. The immediate proximity and wide range of neighboring cells create a favorable environment for horizontal gene transfer (HGT). We focus on gene mobility as it rapidly changes genome plasticity and greatly influences microbial populations in nature and specifically, in gut environments. Plasmids are major mediators of HGT, contributing greatly to genome evolution. Virulence factors, as well as antibiotic-resistance genes, are frequently transferred on plasmids, enabling their rapid spread within and between bacterial populations. Our fascination with this topic, together with a lack of tools for its study, led us to develop a procedure of metagenomic plasmid isolation and characterization. This pioneering approach provides an overview of plasmids—their identity, traits and the phylogenetic diversity of their microbial hosts. Understanding the role of plasmids as carriers of genetic information is crucial to our understanding of microbial ecology and evolution.
WHAT WE PUBLISHED?
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2021
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2015
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2011
Click on Title to View Article
OUR LAB LIFE
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Lab Retreat 10-12/09Excavations at Timna Park 13/01/22BBQ at Omer’s 27/10/21Lab retreat to northern Israel 31/05-01/06Masquerade BBQ at Itzik’s place 4/11/20Lab BBQ at Itzik’s 17/6/20Thai street food cooking class! 20/11/19Lab Poyke at Itzik’s firepit 15/5/19
ALUMNI
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Currently: PI at the ARO, Volcani Center
Motto: Lets talk about it, even though I’m right
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Currently: Assistant professor Whchinigen university Netherlands
Motto: You can always swim your way out of it
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Currently: Scientist at “Evogene”
Motto: Kindness is a virtue
ashkenai@post.bgu.ac.il -
Currently: Researcher and consultant at the Ministry of Agriculture
Motto: No worries
yoav.shaani@mail.huji.ac.il
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Currently: CTO & Co-Founder – BioTech Elements
Motto: “Ask, believe, receive” -Rhonda Byrne “The Secret”
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Currently: Bioinformatics Analyst at BiomX Ltd
Motto: Beer. Now there’s a temporary solution.
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Currently: Head of computational human microbiome research at Biomica Ltd
Motto: The only way is up
sheerlik@yahoo.com
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Currently: Independent
Motto: Mark the target, I will get there
Hobbies: Growing children
frinir.1@gmail.com -
Currently: Profesor university of Estadual de Maringá Brazil
Motto: I did not say it would be easy, I said it would worth it
thomerdurman@hotmail.com -
Research interests: Rumen plasmids
maraikep@post.bgu.ac.il
Motto: Phenomenal cosmic powers. Itty-bitty living space
Hobbies: Moving fast -
Research interests: Genome Assembly
Motto: Stand back – I’m gonna try science!
Hobbies: Drowning (water, data, ice-cream, you name it…)
sasha.kugel@gmail.com -
Research interests: Characterization of rumen plasmids
Motto: Get to the point
Hobbies: Kite surfing
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Research interests: Rumen metagenomics
Motto: There must be an easier and smarter way to do it
Hobbies: In my spare time I like to practice modern dance
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Research interests: Characterization of rumen methanogens
Motto: There is order in everything
Hobbies: Smiling
adi.israel84@gmail.com
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Research interests: Metabolic engineering
Motto: There is order in chaos
Hobbies: Collecting reptiles
l_eitai@yahoo.com -
Motto: You cannot discover new oceans unless you have the courage to lose sight of the shore
Hobbies: Traveling, basketball, playing guitar
chagaida@post.bgu.ac.il
CONTACT US
Address
Ben-Gurion University of the Negev,
Faculty of Natural Sciences, Life Sciences, building 41, room 228Phone
08-6479836/7/8
Fax
08-6479839
Email
imizrahi@bgu.ac.il
We believe in synergism and complementation between people as a driving force for great ideas and fun.
We look for talented enthusiastic students which are curiosity driven.
M.Sc , PhD and post doc positions are available.