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Articles since 2013


 Research 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. 


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.


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. (2019). Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nature Microbiology. 4(1):177-186. Featured in Nature Microbiology News and Views.


Kolodny O., Weinberg M., Reshef L., Harten L., Hefetz A., Gophna U., Feldman M.W., Yovel Y. Coordinated change at the colony level in fruit bat fur microbiomes through time. Nature Ecology and Evolution. 2019 Jan;3(1):116-124. Featured in Nature’s Research Highlights and Nature Ecology and Evolution News and Views.


Lavy O., Gophna U., Gefen E., Ayali A. The Effect of Density-Dependent Phase on the Locust Gut Bacterial Composition. Frontiers in Microbiology 2019 18;9:3020.





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.