Rotem Bartuv
My work focuses on the application of constraint-based modeling to predict microbial phenotypes and community interactions in agricultural environments. I specialize in the reconstruction and curation of genome-scale metabolic models and the analysis of omics data. My research philosophy centers on coupling in-silico predictions with targeted experimental validation to elucidate complex biological phenotypes that are difficult to observe through experimentation alone.
Current Project:
Developing a computational framework to model the apple carposphere ecosystem. By reconstructing metabolic models for the native apple microbial community and the pathogen P. expansum, I utilize dynamic Flux Balance Analysis (dFBA) to simulate community dynamics and inter-species competition for fruit-specific nutrients.
My work aims to distinguish between different modes of microbial antagonism such as metabolic resource competition and non-metabolic inhibition- such as the secretion of volatile organic compounds (VOCs) and secondary metabolites.
This research provides a predictive platform for identifying effective biocontrol agents and understanding the ecological constraints that shape microbiome structure on harvested fruit.
Education:
Ph.D. Student at the Department of Agroecology and Plants Health| Faculty of Agriculture, The Hebrew University of Jerusalem, Newe Ya'ar Center, Institute of Plant Sciences, The Agricultural Research Organization
2019 - Estimated graduation date: 2023
Advisors: Prof. Droby Samir, Ph.D. Freilich Shiri, ARO Volcani Research Center.
Ph.D. thesis: Using genomics to study the microbiome's function in the disease process in apple fruit after harvest.
Master's thesis: Using genomics decipher eco-system function and design sustainable agricultural and bio-control practices.
Biotechnology, B.Sc.| Faculty of Sciences and Technology, Tel-Hai College 2019– 2016
Specialization in Agriculture.
Short CV:
10.2021-currently:
Practicing a genomics course | Faculty of Agriculture, The Hebrew University of Jerusalem |
The course focuses on the latest sequencing technologies that allow for the creation of genomic-scale data that require developing new methods for processing and analyzing information.
03.2018-10.2019:
Research Assistant | MIGAL- Galilee Research Institute |
Research assistant in the Plant Molecular Genetics laboratory of Prof. Martin Goldway.
Publications:
Abdelfattah, A., Freilich, S., Bartuv, R., Zhimo, V.Y., Kumar, A., Biasi, A., Salim, S., Feygenberg, O., Burchard, E., Dardick, C. and Liu, J., 2021. Global analysis of the apple fruit microbiome: are all apples the same?. Environmental Microbiology, 23(10), pp.6038-6055.
https://doi.org/10.1111/1462-2920.15469
Tal, O., Bartuv, R., Vetcos, M., Medina, S., Jiang, J. and Freilich, S., 2021. NetCom: a network-based tool for predicting metabolic activities of microbial communities based on interpretation of metagenomics data. Microorganisms, 9(9), p.1838.
Zhimo, V.Y., Kumar, A., Biasi, A., Abdelfattah, A., Sharma, V.K., Salim, S., Feygenberg, O., Bartuv, R., Freilich, S., Whitehead, S.R. and Wisniewski, M., 2022. Assembly and dynamics of the apple carposphere microbiome during fruit development and storage. Frontiers in Microbiology, 13, p.928888.
https://doi.org/10.3390/microorganisms9091838
Bartuv, R., Berihu, M., Medina, S., Salim, S., Feygenberg, O., Faigenboim‐Doron, A., Zhimo, V.Y., Abdelfattah, A., Piombo, E., Wisniewski, M. and Freilich, S., 2023. Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples. Environmental Microbiology, 25(9), pp.1728-1746.
https://doi.org/10.1111/1462-2920.16353
Droby, S., Zhimo, V.Y., Sharma, V.K., Bartuv, R., Wisniewski, M., Zhang, H., Freilich, S. and Spadaro, D., 2026. A hidden alliance: The potential role of bacteria in the virulence of postharvest fungal pathogens. Postharvest Biology and Technology, 234, p.114130.