Prof. Uri Gophna

מקרוביולוגיה מולקולרית סגל אקדמי בכיר
Prof. Uri Gophna
Phone: 03-6409988
Another phone: 03-6406646
Fax: 03-6409407
Office: Green - Biotechnology, 121



1998-2003 Ph.D; Microbiology (with distinction), Tel Aviv University
1995-1998 M.Sc.; Biotechnology (magna cum laude), Tel Aviv University
1992-1996 B.Sc.; Biotechncology and Food Engineering (magna cum laude), Technion-Israeli Institute of Technology


Academic Appointments:


2017- Present  Full Professor, School of Molecular Cell Biology and Biotechnology, Tel Aviv University 
2012-2017 Associate Professor, Dept of Molecular Microbiology and Biotechology, Tel Aviv University
2007-2012 Senior Lecturer, Dept of Molecular Microbiology and Biotechology, Tel Aviv University
2006-2007 Ph.D. level Instructor, Dept of Molecular Microbiology and Biotechology, Tel Aviv University
2005-2006 Postdoctoral Fellow, Tel Aviv University
2003-2005 Postdoctoral training, Dalhousie University, Halifax, Canada


Honors and Awards:

2018 Member elect,  European Academy of Microbiology
2015 Kavli fellow (National Academy of Sciences, USA)
2008 The Nili Rubinovich-Grossman memorial award (ISM) 
2006-2007 The George S. Wise postdoctoral fellowship
2003-2005 The Killam Postdoctoral Fellowship
2000, 2002 The Joan and Jaim Constantiner Institute for Molecular Genetics Travel Scholarship
2002 The Kaplun Scholarship Award
2001 The Wolf Doctoral Fellowship Award199
1998, 2000 The Award for Research and Teaching Excellence in Medicine and Life Sciences

Professional Activities:

2007 – 2014 Editorial board member for "The Open Evolution Journal".
2009 – 2014 Advisory committee member  – Horizontal gene transfer and between phyla relationships, part of the National Science Foundation (USA),  "Assembling the Tree of Life" Program.
2011 - 2015 Board member Israeli Society for Microbiology.
2011 - date Associate editor – Frontiers in Genetics
2011 - date

Editorial board member – Gut Microbes.

2012 - date Associate editor - BMC Evolutionary Biology.
2015 - date Editorial board member – Scientific Reports
2013 - date Editorial board member – Biology Direct.


Research Interests

Broadly, our research interests revolve around two related topics: 1. The role of lateral (horizontal) gene transfer in the evolution of microorganisms and 2. The study of host-microbe interactions, with particular focus on the human gut microbiome in health and disease. We are interested in fundamental questions in microbial ecology and evolution: What are the factors that drive or limit gene flow between prokaryotic species? How were the first eukaryotes formed? How does host specificity evolve? Which forces shape the population structure of microbial communities in the mammalian microbiota? Which microbial species can cause chronic diseases?

Microbial ecology in health and disease: The human microbiota has been attracting tremendous interest since there is increasing evidence supporting the involvement of the gut microbiota in several human diseases: from inflammatory bowel diseases, colorectal cancer and irritable bowel syndrome to metabolic syndrome and cardiovascular disease.

Impact of horizontal gene transfer on microbial evolution: Using a variety of bioinformatic approaches we identify laterally transferred genes and study their evolution. We also investigate why some gene functions are transferred frequently while others are only rarely horizontally acquired. We also study barriers to gene transfer, in particular the microbial immune system - CRISPR-Cas.

Please read my more detailed research description.


Recent Publications

For the full list


Articles since 2013


Reserach Articles


Pasternak Z., Pietrokovski S., Rotem O., Gophna U., Lurie-Weinberger M.N., Jurkevitch E. (2013). By their genes ye shall know them: genomic signatures of predatory bacteria. ISME J. 7(4):756-69. 

Or, A., Commay, O. and Gophna, U. (2013) In situ transplant analysis of free-living bacteria in a lotic ecosystem. Research in Microbiology 164(3):262-9.

Kaminski, L., Lurie-Weinberger, M.N., Allers, T., Gophna, U., and Eichler J. (2013) Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea. Molecular Phylogenetics and Evolution. 68: 327-339.

Pelchovich, G., Zurvalev, A. and Gophna, U. (2013). Effect of ribosome-targeting antibiotics on streptomycin-resistant Mycobacterium mutants in the rpsL gene. International Journal of Antimicrobial Agents. 42: 129-132. 

Pelchovich, G., Schreiber, R., Zurvalev, A. and Gophna, U. (2013). The contribution of common rpsL mutations in Escherichia coli to sensitivity to ribosome targeting antibiotics. International Journal of Medical Microbiology. 303(8):558-62.


Naor, A., Yair, Y., and Gophna, U. (2013) A halocin-H4 mutant Haloferax mediterranei strain retains the ability to inhibit growth of other halophilic archaea. Extremophiles. 17: 973-979.

Pasternak, Z., Njagi, M., Shani, Y., Chanyi, R., Rotem, O., Lurie-Weinberger, MN, Koval, S., Pietrokovski, S. Gophna, U., and Jurkevitch, E. (accepted). In and out: an analysis of epibiotic vs periplasmic bacterial predators. ISME Journal.

Amir, I., Konikoff, F.M., Oppenheim, M., Gophna, U.* and Half, E.E. (2014) Gastric Microbiota is Altered in Esophagitis and Barrett's Esophagus and Further Modified by Proton Pump Inhibitors. Environmental Microbiology 16(9):2905-14. * Corresponding author

Goldberg E., Amir I., Zafran M., Gophna U., Samra Z., Pitlik S., and Bishara J. (accepted) The correlation between Clostridium difficile infection and human gut concentrations of Bacteroidetes phylum and clostridial species. European Journal of Clinical Microbiology and Infectious Diseases.

Pelchovich, G., Omer-Bendori. S., and Gophna, U. (2013) Menaquinone and iron are essential for complex colony development in Bacillus subtilis. PLoS ONE. 8(11):e79488.

Wagner, A., Zarecki, R., Reshef, L., Gochev C., Sorek R., Gophna U., and Ruppin, E. (2013) Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious. PNAS. 110(47):19166-71.

Shifman, A., Ninyo N., Gophna U., and Snir S. (2014) Phylo SI: a new genome-wide approach for prokaryotic phylogeny. Nucleic Acid Research. 42(4):2391-404.

Amir, I., Bouvet, P., Legeay, C., Gophna, U. and Weinberger, A., (2014) Eisenbergiella tayi gen. nov., sp. nov., isolated from human blood. International Journal of Systematic and Evolutionary Microbiology. 64:907-14.

Or, A., and Gophna U. (2014). Investigating a lotic microbial community following a severe detergent spill. Archives of Microbiology 2:119-124.


Chimileski, S., Dolas, K., Naor, A., Gophna, U., and Papke, R.T. (2014) Extracellular DNA metabolism in Haloferax volcanii. Frontiers in Microbiology. 20; 5:57.


Zerulla, K. Chimileski, S., Nather, D., Gophna, U., Papke, R.T., and Soppa, J. (2014) DNA as a Phosphate Storage Polymer and the Alternative Advantages of Polyploidy for Growth or Survival. PLoS One 9: e94819. Frontiers in Microbiology.


Zarecki, R., Oberhardt, M.A.,  Yizhak, K., Wagner, A., Shtifman-Segal, E., Freilich, S., Henry, C.S., Gophna, U., Ruppin, E.(2014) Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms. PloS One 9):e98372.


Eilam, O. Zarecki, R., Oberhardt, M.A.,  Ursel, L.K., Kupiec, M., Knight, R., S., Gophna, U., Ruppin, E.(2014). Glycan Degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. mBIO 5 (4), e01526-14.


Pelchovich, G., Nadejda, S., Dana, A., Tuller, T., Bravo, I.G., and Gophna, U. (2014) Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS Journal 281 (16), 3701-3718.


Zarecki, R., Oberhardt, M.A.,  Reshef, L.,  Gophna, U., Ruppin, E. (2014) A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness. PLoS computational biology 10 (7), e1003726.


Gophna, U, Kristensen, DM, Wolf YI, Popa O, Drevet C, Koonin EV (2015). evidence of inhibition of horizontal gene transfer by CRISPR-Cas on evolutionary timescales. ISME Journal. (9), 2021–2027.


Reshef, L., Kovacs, A., Ofer, A., Yahav, L.,  Keren, N., Maharshak, N., Konikoff, F.M., Tulchinsky, H., Gophna, U.* and Dotan, I*. (accepted) Pouch Inflammation is Associated with a Decrease in Specific Bacterial taxa. Gastroenterology.  *Corresponding authors


Dan, M., Yair, Y., Samosav, A., Gottesman, T., Yossepowitch, O. Harari-Schwartzd, O., Tsivian, E., Schreiber, R., Gophna, U. (2015) Escherichia coli isolates from patients with bacteremic urinary tract infection are genetically distinct from those derived from sepsis following prostate transrectal biopsy. International Journal of Medical Microbiology.(4-5):464-8.


Roterman, Y.R., Benayahu, Y., Reshef, L., Gophna, U. (2015) The gill microbiota of invasive and indigenous Spondylus oysters from the Mediterranean Sea and northern Red Sea. Environmental Microbiology Reports. 7 (6), 860-867


Keren, N., Konikoff, F.M., Paitan, Y.,  Gabay, G., Reshef, L., Naftali, T., Gophna, U. (2015) Interactions between the intestinal microbiota and bile-acids in gallstones patients. Environmental Microbiology Reports. 7 (6), 874-880.


Oberhardt, M.A., Zarecki, R., Gronow, S., Lang, E., Klenk, H.P., Gophna, U*., and Ruppin, E*. (2015) Harnessing the landscape of microbial culture media to predict new organism-media pairings. Nature Communications. 13;6:8493.* Corresponding authors.


Ninio, N., Adato, O., Gophna, U. and Snir, S. Detecting Horizontal Gene Transfer Between Closely Related Taxa. (2015). PLoS Computational Biology 6;11(10):e1004408.


Naftali, T., Reshef, L., Kovacs, A., Porat, R., Amir, I., Konikoff, F.M., and Gophna, U. (2016) Distinct microbiotas are associated with ileum-restricted and colon-involving Crohn's Disease. Inflammatory Bowel Diseases. 22(2):293-302


Oberhardt, M.A., Zarecki, R., Reshef, L., Xia, F., Duran-Frigola, M., Schreiber, R., Henry, C.S., Ben-Tal, N., Dwyer, D.J*., Gophna, U*., and Ruppin, E* (2016). Systems-wide prediction of enzyme promiscuity reveals a new underground alternative route for pyridoxal 5’-phosphate production in E. coli. PLoS Computational Biology 12(1):e1004705.


Yanuka-Golub, K., Reshef, L., Rishpon, Y. and Gophna, U. (2016) Community structure dynamics during startup in microbial fuel cells–the effect of phosphate concentrations. Bioresource Technology 6;212:151-159


Naor, A., Altman-Price, N., Soucy, S.M., Green, A.G., Mityagin, Y., Turgeman, I., Davidovich, N., Gogarten, J.P.*,  and Gophna, U*. Impact of a homing intein on recombination frequency and organismal fitness (2016). PNAS. 113(32): E4654–E4661. * Corresponding authors


Maharshak, N., Cohen, N.A., Reshef, L., Tulchinsky, H., Gophna, U. and Dotan, I. (2017) Alterations of enteric microbiota in patients with a normal ileal pouch are predictive of pouchitis. Journal of Crohn's and Colitis. 11(3):314-320.


Gophna, U., Konikoff, T, and Nielsen, H.B. (2017) Oscillospira and related bacteria – from metagenomic species to metabolic features. Environmental Microbiology 19(3):835-841

Stachler, A.E., Turgeman-Grott, I., Shtifman-Segal,E., Allers, T., Marchfelder, A. *, Gophna, U.*   (2017) High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon. Nucleic Acids Research. 45(9):5208-5216. * Equal contribution

Artieri, C.G., Naor, A., Turgeman-Grott, I., Zhou, Y., York, R., Gophna, U., Fraser H.B. (2017) Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids. Scientific Reports 7(1):3986.

Shalev Y., Turgeman-Grott I., Tamir A., Eichler J., and Gophna U. (2017) Cell Surface Glycosylation Is Required for Efficient Mating of Haloferax volcanii. Frontiers in Microbiology. 2017 Jul 5;8:1253. 


Shalev Y., Soucy S.M., Papke R.T., Gogarten J.P., Eichler J., and Gophna U. (2018) Comparative Analysis of Surface Layer Glycoproteins and Genes Involved in Protein Glycosylation in the Genus Haloferax. Genes. 20;9(3). pii: E172.


Shulman A., Yair Y., Biran D., Sura T., Otto A., Gophna U., Becher D., Hecker M., Ron E.Z.. (2018). The Escherichia coli Type III Secretion System 2 Has a Global Effect on Cell Surface. MBio. 2018 3;9(4). pii: e01070-18.


Yitzhaki S., Reshef L., Gophna U., Rosenberg M., Sterer N. (2018) Microbiome associated with denture malodour. Journal of Breath Research. Jan 17;12(2):027103. doi: 10.1088/1752-7163/aa95e0.


Turgeman-Grott, I., Joseph, S., Marton, S., Eizenshtein, K., Naor, A., Soucy, S.M., Stachler, A.E., Shalev, Y., Zarkor,M., Reshef, L., Altman-Price, N, Marchfelder, A., and Gophna, U. (2018). Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation (accepted). Nature Microbiology.





Lurie-Weinberger, M. N., and Gophna, U. (2015) Archaea in and on the human body - health implications and future directions PLoS Pathogens. 11;11(6):e1004833.


Konikoff, T, and Gophna, U. Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota (2016). Trends in Microbiology 24(7):523-4.


Gophna, U.,  Allers, T., and Marchfelder, A. (2017) Finally, Archaea Get Their CRISPR-Cas Toolbox‏ Trends in Microbiology 25(6):430-432.


Gophna U. and Yair Y. (2018)  Repeat modularity as a beneficial property of multiple CRISPR-Cas systems. RNA Biol. 10:1-3. 


Maier L.K., Stachler A.E., Brendel J., Stoll B., Fischer S., Haas K.A., Schwarz T.S., Alkhnbashi O.S., Sharma K., Urlaub H., Backofen R., Gophna U., and Marchfelder A. (2018) The nuts and bolts of the Haloferax CRISPR-Cas system I-B. RNA Biol. 21:1-12


Tel Aviv University makes every effort to respect copyright. If you own copyright to the content contained
here and / or the use of such content is in your opinion infringing, Contact us as soon as possible >>