Microbes Are Everywhere

We study what makes them live together

Microbes Are Everywhere

We study what makes them live together

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.

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.

ongoing projects

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.
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.
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.
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.

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Who We Are?

Lab Life

Alumni

Courses

Computational Microbial Ecology

This bioinformatics course equips students with the tools and knowledge to analyze microbial communities through hands-on experience with software like QIIME and exploration of genome analysis, diversity assessment, and community functionality. By combining theoretical understanding with practical application, students will gain expertise in dissecting complex microbial ecosystems and interpreting their roles and functions in various environments.

Microbial Ecology

This course delves into the fascinating world of microbes and their environments, exploring their interactions, roles, and impact on health and disease. Students will learn to analyze and predict microbial behavior, engineer changes for beneficial outcomes, and tackle real-world challenges in microbial ecology.

Contact Us

Address
Ben-Gurion University of the Negev, Faculty of Natural Sciences, Life Sciences, building 41, room 228

Phone
08-6479836/7/8

Fax
08-6479839

Mail
imizrahi@bgu.ac.il