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Peer-reviewed Publications

Click here for a full list of all publications,

below are articles we've published since 2015. 

Articles since 2015 (Names of Gophna lab members are highlighted)


Research Articles

Lapidot, Y., Reshef, L., Mayan, M., Cohen, D., Gophna, U. Muhsen, K. (2022). Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children. NPJ Biofilms Microbiomes. 3;8(1):10.

Alarcón-Schumacher, T., Naor, A.,  Gophna, U., Erdmann, S. (2022) Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. PNAS 119 (35), e2205037119

Bar N., Avraham Y., Dubinsky V., Cohen N.A., Weiss G.A., Banon L., Tulchinsky H., Maharshak N., Gophna U., Dotan I. (2022). Long-term Antibiotic Treatment in Pouchitis-Patterns of Use and Safety. Inflammatory Bowel Diseases 1;28(7):1027-1033.

Lavy O., Lewin-Epstein O., Bendett Y., Gophna U., Gefen E., Hadany L., Ayali A. (2022) Microbiome-related aspects of locust density-dependent phase transition. Environmental Microbiology 24(1):507-516.

Dubinsky V., Reshef L., Rabinowitz K., Wasserberg N., Dotan I., Gophna U. (2022) Escherichia coli strains from patients with inflammatory bowel diseases have disease-specific genomic adaptations.  Journal of Crohn's and Colitis. 16 (10), 1584-1597

Harel, N. Reshef, L., Biran, D., Brenner, S.. Ron, E.Z., Gophna U. (2022) Effect of Solar Radiation on Skin Microbiome: Study of Two Populations. Microorganisms 10 (8) 1523

Neri, U., Wolf, Y.I, Roux, S., Camargo, A.P., Lee, B., Kazlauskas, D., Min Chen, I., Ivanova, N. Zeigler Allen, L., Paez-Espino, D., Bryant, D.A., Bhaya, D., RNA Virus Discovery Consortium, Krupovic, M., Dolja, V.D., Kyrpides, N.C*., Koonin, E.V.*, Gophna U*. (2022) Expansion of the global RNA virome reveals new clades of bacteriophages. Cell 185 (21), 4023-4037

Godny, L.,  Reshef, L.,  Sharar Fischler, T., Elial-Fatal, S., Pfeffer-Gik, T., Raykhel, B., Rabinowitz, K., Levi-Barda, A., Perets, T.T.,  Barkan, R., Goren, I., Ollech, J.E., Yanai, H., Gophna, U., Dotan, I. (2022) Increasing adherence to the Mediterranean diet and lifestyle is associated with reduced fecal calprotectin and intra-individual changes in microbial composition of healthy subjects. Gut Microbes 14 (1), 2120749.



Yanuka-Golub, K., Dubinsky, V., Korenblum, E., Reshef, L., Ofek-Lalzar, M., Rishpon, J., and Gophna, U. (2021) Anode Surface Bioaugmentation Enhances Deterministic Biofilm Assembly in Microbial Fuel Cells. mBIO 12(2):e03629-20.

Dubinsky, V., Reshef, L., Rabinowitz, K., Yadgar, K., Godny, L., Zonensain, K., Wasserberg, N., Dotan, I. and Gophna, U., (2021). Dysbiosis in metabolic genes of the gut microbiomes of patients with an ileo-anal pouch resembles that observed in Crohn's Disease. mSystems 2(6):e00984-20.


Ryvchin, R., Dubinsky, V., Rabinowitz,K., Wasserberg, N.,  Dotan, I., and Gophna, U. (2021) Alteration in urease-producing bacteria in the gut microbiomes of patients with inflammatory bowel diseases. Journal of Crohn's and Colitis 18;15(12):2066-2077.


Lavy, O., Gophna, U., Ayali, A., Gihaz, S. Fishman, A., Gefen, E. (2021) The maternal foam plug constitutes a reservoir for the desert locust's bacterial symbionts Environmental Microbiology 23 (5), 2461-2472.

Feng, Y., Neri, U., Gosselin, S., Louyakis, A.S., Papke, R.T., Gophna, U., and Gogarten, J.P. (2021). The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biology and Evolution. 13(8):evab166.

Lapidot, Y., Reshef, L., Goldsmith, R., Na’amnih, W., Kassem, E., Ornoy, A., Gophna, U. Muhsen, K. (2021). The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence. Nutrients 13(8):2645.


Meir, M., Harel, N., Miller, D. Gelbart, M., Eldar, A., Gophna, U.,* and Stern, A.* (2020) Competition between social cheater viruses is driven by mechanistically different cheating strategies. Science Advances 21;6(34) * Corresponding authors

Babakobi M.D., Reshef L., Gihaz S., Belgorodsky B., Fishman A., Bujanover Y., Gophna U. (2020) Effect of Maternal Diet and Milk Lipid Composition on the Infant Gut and Maternal Milk Microbiomes. Nutrients 21;12(9):E2539. 

Robinzon S., Cawood A.R., Ruiz M.A., Gophna U., Altman-Price N., Mills K.V. (2020) Protein splicing activity of the Haloferax volcanii PolB-c intein is sensitive to homing endonuclease domain mutations. Biochemistry 59, 36, 3359–3367.

Stachler A.E., Wörtz J., Alkhnbashi O.S., Turgeman-Grott I., Smith R., Allers T., Backofen R., Gophna U., Marchfelder A. (2020) Adaptation induced by self-targeting in a type I-B CRISPR-Cas system. Journal of Biological Chemistry 25; 295(39): 13502–13515.

Dubinsky, V., Reshef, L., Bar, N., Keizer, D., Golan, N., Rabinowitz, K., Godny, L., Yadgar, K., Zonensain, K., Tulchinsky, H., Gophna, U., and Dotan, I. (2020). Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy. Gastroenterology 158(3):610-624.


Turner D., Bishai J., Reshef L., Abitbol G., Focht G., Marcus D., Ledder O., Lev-Tzion R., Orlanski-Meyer E., Yerushalmi B., Aloi M., Griffiths AM., Albenberg L., Kolho KL., Assa A., Cohen S., Gophna U., Vlamakis H., Lurz E., Levine A. (2020)  Antibiotic Cocktail for Pediatric Acute Severe Colitis and the Microbiome: The PRASCO Randomized Controlled Trial. Inflammatory Bowel Diseases. 26(11):1733-1742.

Yair Y., Borovok I., Mikula I., Falk R., Fox L.K., Gophna U., Lysnyansky I. (2020) Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel. BMC Genomics 21(1):70. 


Lavy O., Gophna U., Gefen E., Ayali A. (2020) Dynamics of bacterial composition in the locust reproductive tract are affected by the density-dependent phase. FEMS Microbiology Ecology. 96(4).


Godny L., Reshef L., Pfeffer-Gik T., Goren I., Yanai H., Tulchinsky H., Gophna U., Dotan I. (2020) Adherence to the Mediterranean diet is associated with decreased fecal calprotectin in patients with ulcerative colitis after pouch surgery. European Journal of Nutrition. 59:3183–3190.



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; Editor’s Choice in Microbiology - The Scientist magazine.

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. (2019) The Effect of Density-Dependent Phase on the Locust Gut Bacterial Composition. Frontiers in Microbiology18;9:3020.

Yanuka-Golub, K., Baransi-Karkaby, K., A., Szczupak, A., L Reshef, L., Rishpon, J. Shechter, R.,  Gophna, U., Sabbah. I. (2019). An electrode-assisted anaerobic digestion process for the production of high-quality biogas. Water Science and Technology  79 (11): 2145-2155.

Goren I., Godny L., Reshef L., Yanai H., Gophna U., Tulchinsky H., Dotan I. (2019) Starch Consumption May Modify Antiglycan Antibodies and Fecal Fungal Composition in Patients With Ileo-Anal Pouch. Inflammatory Bowel Diseases. 14;25(4):742-749.


Harel, N., Meir, M., Gophna, U., and Stern, A. (2019). Direct Sequencing of RNA with MinION Nanopore: Detecting Mutations based on Associations. Nucleic Acids Research. 16;47(22):e148.

Half E., Keren N., Reshef L., Dorfman T., Lachter I., Kluger Y., Reshef N., Knobler H., Maor Y., Stein A., Konikoff F.M., Gophna U. (2019) Fecal microbiome signatures of pancreatic cancer patients. Scientific Reports 14;9(1):16801.



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.



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.


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.


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.

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.


Gophna, U., Kristensen, DM, Wolf YI, Popa O, Drevet C, Koonin EV (2015). No 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. (2015) Pouch Inflammation is Associated with a Decrease in Specific Bacterial taxa. Gastroenterology. 149(3):718-27.


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.


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

Reviews and commentaries




Gophna, U. Et tu, Vibrio cholerae? Kin-cannibalism and a bacterial secretion system. Cell 185 (22), 4039-4040


Gophna U., Altman-Price, N.  (2022). Horizontal Gene Transfer in Archaea - From Mechanisms to Genome Evolution. Annual Review of Microbiology 76:481-502


Dubinsky V., Dotan I., Gophna U. Carriage of Colibactin-producing Bacteria and Colorectal Cancer Risk. (In press) Trends in Microbiology

Gophna U. (2020) Reviewing the right papers. FEMS Microbiol Lett. 1:367(1).

Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, Gophna U, Kishony R, Molin S, Tønjum T. (in press) Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol Rev. ​



Gophna U. (2018) The unbearable ease of expression-how avoidance of spurious transcription can shape G+C content in bacterial genomes. FEMS Microbiol Lett. 1;365(23).


Yair Y, Gophna U. (2018) Pandemic Bacteremic Escherichia Coli Strains: Evolution and Emergence of Drug-Resistant Pathogens. Curr Top Microbiol Immunol. 416:163-180.


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


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




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



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


Lurie-Weinberger, M.N., and Gophna, U. (2015) Archaea in and on the human body - health implications and future directions PLoS Pathogens. 11(6): e10048339.

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