Prof. Uri Gophna

Education:
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:
2023		Elected member, EMBO
2020		Elected member, American Academy of Microbiology
2019		Sarov Prize for basic research (Israeli Society for Microbiology)
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
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.

 

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.

 

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.

 

 

Reviews

 

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