Meet our team
I am an evolutionary microbiologist, focused on horizontal gene transfer in archaea and bacteria, and mechanisms that restrict it. I am fascinated with how mobile elements end up shaping the evolutionary fate of microbial lineages, and although inherently selfish, sometimes contribute greatly to adaptive processes within ecosystems.
In the recent past, I have characterized virulence factors of E. coli that cause bloodstream infections, and reconstructed their likely source. Nowadays I study the growth phenotypes of recombinant hybrids in archaea that have chimeric genomes - part H. mediterranei/part H. volcanii, under different conditions, to better understand risks and benefits of HGT . I also teach undergrad and graduate students the basic molecular biology techniques, take care of lab safety, and manage the lab accounts.
Postdoctoral Research Associate
CRISPR-Cas systems provide acquired heritable immunity to bacteria and archaea against invasion by selfish DNA elements. I observed that many halophilic archaea have spacers that target chromosomal replication genes, implying a potential role for CRISPR-Cas in interspecies antagonism and genetic conflicts in archaea. Currently, I am finding out how such spacers are acquired, and their affects on lateral gene transfer in these organisms
Mating by fusion in halophilic archaea has been known for over 25 years but the mechanisms behind it are completely unknown. I am investigating a number of potential mechanisms that enable fusion. In terms of the first step in mating, cellular recognition, I am studying how different S-layer proteins and different patterns of surface glycosylation affect cell-cell recognition and mating efficiency in Haloferax species.
Postdoctoral Research Associate
When I first entered the field after a thesis in classical microbiology, Uri promised me I would never get bored. Five years later. that still holds true. I direct and advise all microbiome analysis going on in the lab, which can span a broad spectrum from oysters to humans. As the entire field is moving forward at breakneck pace, this sometimes feels like trying to solve a jigsaw puzzle while riding a roller-coaster, but, it's an exhilarating ride all the way.
I will soon be starting a rotation studying viruses and CRISPR in archaea and how they interact.
I study the RNA bacteriophage MS2 and try to turn it into a system to study evolutionary fitness landscapes. On the way to engineering this phage, I have discovered new details of the molecular biology of its interactions with the E. coli host.
My thesis work will be focusing on addressing the functions of CRISPR-Cas system beyond defense mechanism, which includes the role of CRISPR-Cas in gene exchange across different species and its impact on microbial speciation, primarily in halophilic archaea.
CRISPR-Cas is a prokaryotic defense system that could limit gene transfer and is able to reduce the virulence and the antibiotic resistance of pathogenic strains. However, CRISPR-Cas systems may have other functions beyond dynamic immunity. My research is focused on the pathogenic strains Neisseria eningitidis and Neisseria gonorrhoeae. I am characterizing the CRISPR systems of those strains using bioinformatics analysis. I aim to find if there are unknown roles of the CRISPR systems in those bacteria.
Postdoctoral Research Associate
I am using a wide array of bioinformatic approaches to identify the targets of CRISPR spacers in metagenomes to gain a fuller understanding of their ecological and evolutionary importance. I am also studying the dynamics of CRISPR spacer acquisition and loss, in halophilic mesocosms that we have established in the lab.
Archaea that were isolated from hypersaline water in Atlait along with a symbiotic virus show an increased growth rate phenotype. My research focuses on discovering which genes in the symbiotic virus are involved in this phenotype. In addition, we investigate whether the symbiotic virus has also anti-CRISPR activity.
In my research, I am studying the CRISPR-Cas system and its role in genome stability in haloarchaea. Different mutants in case genes in Haloferax volcanii show different DNA-damage related phenotypes, which I am currently characterizing.
My research focuses on the bacterium Enteroaggregative E. coli (EAEC) and how its virulence traits correlate with other bacteria in the gut microbiome. ETEC is a gut pathogen infecting adults and children worldwide. It may lead to chronic inflammation, burdening children in developing nations. My efforts are to approach this topic from the data analysis perspective; by applying machine learning techniques. My free time interests are Japanese archery (弓道), swimming, and sour bread baking.
IBD is a group of chronic inflammatory diseases of the gastrointestinal tract, which are associated with significant morbidity. Alteration of the gut microbiota has been implicated in the pathogenesis of IBD. I study the role of bacterial urease in IBD, using metagenomic analysis of fecal samples from various patients.
I study the fascinating field of small RNAs in extra-intestinal pathogenic E. coli (ExPEC). sRNAs were shown to play an important role in regulating virulence associated genes in human pathogens- I focus on ExPEC, which are the leading cause to urinary tract infections, and can cause to life-threatening infections, including sepsis. I aim to identify and study sRNAs participating in the serum response of ExPEC.
I explore the prokaryotic virosphere in two venues:
1. Sampling extreme environments (such as the Dead Sea) and attempting to identify new and exciting viruses and their respected hosts.
2. Utilizing computational methods and publicly available multi-”OMICS” data, in order to expand the known viral gene repertoire.
Vadim (Dani) Dubinsky
My current research focuses on the shotgun metagenomic analysis of the gut microbiome of patients with inflammatory bowel diseases (IBD). By using advanced bioinformatic and statistical methods I analyze large metagenomic and clinical datasets and employ machine learning for microbial biomarkers detection and patients’ stratification. I focus on comparative genomics of commensal species such as Escherichia coli. The outcomes of this research will shed more
light on IBD pathogenesis and mechanisms of antibiotic resistance and hopefully will be translated to clinical benefit.