A5077184904- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Bioinformatics and Genomic Networks
- Reproductive tract infections research
- Pesticide and Herbicide Environmental Studies
- Enzyme Catalysis and Immobilization
- Probiotics and Fermented Foods
- Cervical Cancer and HPV Research
- Viral Infectious Diseases and Gene Expression in Insects
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Anaerobic Digestion and Biogas Production
- Microbial Fuel Cells and Bioremediation
- Genomics and Phylogenetic Studies
- Plant biochemistry and biosynthesis
- Endoplasmic Reticulum Stress and Disease
- Gene Regulatory Network Analysis
- Microbial Metabolites in Food Biotechnology
- Maternal and Perinatal Health Interventions
- Enzyme Structure and Function
- Urinary Tract Infections Management
- Evolutionary Game Theory and Cooperation
- Water-Energy-Food Nexus Studies
Tel Aviv University
2011-2024
Agricultural Research Organization
2018-2024
Hillel Yaffe Medical Center
2022-2023
Ben-Gurion University of the Negev
2021-2022
Technion – Israel Institute of Technology
2020
University of Maryland, College Park
2015
Growing evidence supports the importance of gut microbiota in control tumor growth and response to therapy. Here, we select prebiotics that can enrich bacterial taxa promote anti-tumor immunity. Addition inulin or mucin diet C57BL/6 mice induces immune responses inhibition BRAF mutant melanoma a subcutaneously implanted syngeneic mouse model. Mucin fails inhibit germ-free mice, indicating is required for activation response. Inulin drive distinct changes microbiota, as inulin, but not mucin,...
Abstract Culturing microorganisms is a critical step in understanding and utilizing microbial life. Here we map the landscape of existing culture media by extracting natural-language recipes into Known Media Database (KOMODO), which includes >18,000 strain–media combinations, >3300 variants compound concentrations (the entire collection Leibniz Institute DSMZ repository). Using KOMODO, show that although are usually tuned for individual strains using biologically common salts, trace...
Abstract Accumulating evidence points to an important role for the gut microbiome in anti-tumor immunity. Here, we show that altered intestinal microbiota contributes immunity, limiting tumor expansion. Mice lacking ubiquitin ligase RNF5 exhibit attenuated activation of unfolded protein response (UPR) components, which coincides with increased expression inflammasome recruitment and dendritic cells reduced antimicrobial peptides epithelial cells. Reduced UPR is also seen murine human...
There is a growing demand for genome-scale metabolic reconstructions plants, fueled by the need to understand basis of crop yield and progress in genome transcriptome sequencing. Methods are also required enable interpretation plant data study how cellular activity varies under different growth conditions or even within organs, tissues, developmental stages. Such methods depend extensively on accuracy with which genes have been mapped biochemical reactions pathways. Errors these mappings...
Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these rumen ecosystem - a complex microbial that resides upper digestive tract of ruminant animals and is responsible for degradation ingested plant material. Our dietary intervention experiments revealed affects most abundant taxa within specific group methanogenic archaea order Methanomicrobiales highly sensitive...
Glycans form the primary nutritional source for microbes in human gut, and understanding their metabolism is a critical yet understudied aspect of microbiome research. Here, we present novel computational pipeline modeling glycan degradation (GlyDeR) which predicts potency 10,000 reference glycans based on either genomic or metagenomic data. We first validated GlyDeR by comparing profiles genomes Human Microbiome Project against KEGG reaction annotations. Next, applied to analysis mammalian...
Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands automatically generated genome-scale metabolic models to develop predictor minimal medium requirements, which apply species study relationship between their and ecological genomic traits. We first show that are more similar among co-habit many niches. then reveal three fundamental characteristics fastidiousness (i.e., complex specific requirements): (1)...
Abstract Atrazine is an herbicide and a pollutant of great environmental concern that naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 one the most studied degraders this herbicide. Here, we developed genome scale metabolic model for P. TC1, i RZ1179, to study atrazine degradation process at organism level. Constraint based flux balance analysis time dependent simulations were used explore organism’s phenotypic landscape. Simulations aimed designing media...
Abstract Since the release of ModelSEED in 2010, systems biology research community has used genome-scale metabolic model reconstruction pipeline to build over 200,000 draft reconstructions that support hundreds publications. Here we describe first comprehensive update this tool, with new features such as (i) a dramatically improved representation energy metabolism, which ensures models produce accurate amounts ATP per mol nutrient consumed; (ii) template for Archaea reconstruction; and...
Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such is an important open question in biology. Here we develop a genome-wide method, PROPER, uses permissive PSI-BLAST approach to predict activities metabolic genes. Enzyme promiscuity typically studied experimentally using multicopy suppression, which over-expression 'replacer' gene rescues lethality caused by inactivation 'target' gene. We use PROPER...
Significance Biologists frequently overexpress genes to learn about their cellular functions, and biotechnologists do so construct novel metabolic pathways that produce valuable chemical compounds. However, gene overexpression often leads deleterious consequences whose cause is unclear. Here, we present a computational method named Expression-Dependent Gene Effects (EDGE) can successfully predict the effects resulting from of either native or foreign (originating in another species) genes....
Phenyl urea herbicides are being extensively used for weed control in both agricultural and non-agricultural applications. Linuron is one of the key this family wide use. Like other phenyl herbicides, it known to have toxic effects as a result its persistence environment. The natural removal linuron from environment mainly carried through microbial biodegradation. Some microorganisms been reported mineralize completely utilize carbon nitrogen source. Variovorax sp. strain SRS 16 efficient...
Providing the food requirements of a growing population comes at cost intensive use agrochemicals, including pesticides. Native microbial soil communities are considered key players in degradation such exogenous substances.
Growth rate has long been considered one of the most valuable phenotypes that can be measured in cells. Aside from being highly accessible and informative laboratory cultures, maximal growth is often a prime determinant cellular fitness, predicting underlie fitness key to both understanding manipulating life. Despite this, current methods for microbial typically focus on yields [e.g., predictions biomass yield using GEnome-scale metabolic Models (GEMs)] or notably require many empirical...
This protocol describes the process used to convert >1300 microbial media recipes, listed on website of Leibniz Institute DSMZ \(see: https://www.dsmz.de/?id=441), into a machine readable format, and then read them SQL database.In process, we combine compounds with degenerate names include concentrations all in standard units.The includes steps for errorchecking, as well recursively add when they cross-reference each other.The might be useful other, similar database building tasks,...
<h3>Introduction</h3> Microbiome plays an important role in development of cancer and response to chemotherapy. We aim examine the significance vaginal microbiome epithelial ovarian cancer. <h3>Methods</h3> A prospective cohort study was conducted for evaluating newly diagnosed (NEOC) patients, post-chemotherapy (PC) patients healthy women. Samples were collected using a swab. DNA extracted amplified by PCR universal primers prokaryotic 16S ribosome. Next-generation sequencing taxonomical...
Background Misoprostol treatment for early pregnancy loss has varied success demonstrated in previous studies. Incorporating predictors a single clinical scoring system would be highly beneficial practice. Objective To develop and evaluate the accuracy of to predict misoprostol outcomes managing loss. Study design Retrospective cohort validation study. Methods Patients discharged from gynecologic emergency department 2013 2016, diagnosed with loss, who were treated 800 mcg misoprostol,...
ABSTRACT Atrazine is an herbicide and pollutant of great environmental concern that naturally biodegraded by microbial communities. The efficiency biodegradation can be improved through the stimulating addition fertilizers, electron acceptors, etc. In recent years, metabolic modelling approaches have become widely used as in silico tool for organism-level phenotyping subsequent development engineering strategies including improvement. Here, we constructed a genome scale model, i RZ960,...