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.