Abteilung Umweltmikrobiologie



Bagutti, C., Alt Hug, M., Heim, P., Ilg Hampe, E., Hübner, P., Julian, T. R., … Tschudin-Sutter, S. (2024). Association between the number of symptomatic mpox cases and the detection of mpox virus DNA in wastewater in Switzerland: an observational surveillance study. Swiss Medical Weekly, 154, 3706. doi:10.57187/s.3706, Institutional Repository
Bopp, C. E., Bernet, N. M., Meyer, F., Khan, R., Robinson, S. L., Kohler, H. P. E., … Hofstetter, T. B. (2024). Elucidating the role of O2 uncoupling for the adaptation of bacterial biodegradation reactions catalyzed by Rieske oxygenases. ACS Environmental Au. doi:10.1021/acsenvironau.4c00016, Institutional Repository
Brizzolara, S., Naudascher, R., Rosti, M. E., Stocker, R., Boffetta, G., Mazzino, A., & Holzner, M. (2024). Immiscible Rayleigh-Taylor turbulence: implications for bacterial degradation in oil spills. Proceedings of the National Academy of Sciences of the United States of America PNAS, 121(11), e2311798121 (9 pp.). doi:10.1073/pnas.2311798121, Institutional Repository
Chen, X., Wang, M., Luo, L., An, L., Liu, X., Fang, Y., … Wu, X. L. (2024). High immigration rates critical for establishing emigration-driven diversity in microbial communities. Cell Systems, 15(3), 275-285. doi:10.1016/j.cels.2024.02.001, Institutional Repository
Conforti, S., Holschneider, A., Sylvestre, É., & Julian, T. R. (2024). Monitoring ESBL-Escherichia coli in Swiss wastewater between November 2021 and November 2022: insights into population carriage. mSphere, 9(5). doi:10.1128/msphere.00760-23, Institutional Repository
D’Souza, G. (2024). Verständnis der mikrobiellen Interaktionen beim Abbau von Polysacchariden. Biospektrum, 30(4), 403-406. doi:10.1007/s12268-024-2230-x, Institutional Repository
Gogia, G., & Johnson, D. R. (2024). Bacteria spiral into control. Nature Physics, 20, 897-898. doi:10.1038/s41567-024-02509-w, Institutional Repository
Hamilton, K. A., Ciol Harrison, J., Mitchell, J., Weir, M., Verhougstraete, M., Haas, C. N., … Rose, J. B. (2024). Research gaps and priorities for quantitative microbial risk assessment (QMRA). Risk Analysis. doi:10.1111/risa.14318, Institutional Repository
Julian, T. R., & Boehm, A. B. (2024). Advances in wastewater-based epidemiology in the ES&T family of journals. ACS ES&T Water. doi:10.1021/acsestwater.4c00459, Institutional Repository
Julian, T. R., Devaux, A. J., Brülisauer, L., Conforti, S., Rusch, J. C., Gan, C., … Ort, C. (2024). Monitoring an emergent pathogen at low incidence in wastewater using qPCR: Mpox in Switzerland. Food and Environmental Virology. doi:10.1007/s12560-024-09603-5, Institutional Repository
Lee, K. S., Landry, Z., Athar, A., Alcolombri, U., Pramoj Na Ayutthaya, P., Berry, D., … Stubbusch, A. K. M. (2024). MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. Nature Microbiology, 9, 1152-1156. doi:10.1038/s41564-024-01656-3, Institutional Repository
Nadeau, S., Devaux, A. J., Bagutti, C., Alt, M., Hampe, E. I., Kraus, M., … Stadler, T. (2024). Influenza transmission dynamics quantified from RNA in wastewater in Switzerland. Swiss Medical Weekly, 154(1), 3503 (20 pp.). doi:10.57187/s.3503, Institutional Repository
Probst-Rüd, S., Nyangaresi, P. O., Adeyeye, A. A., Ackermann, M., Beck, S. E., & McNeill, K. (2024). Synergistic effect of UV-A and UV-C light is traced to UV-induced damage of the transfer RNA. Water Research, 252, 121189 (8pp.). doi:10.1016/j.watres.2024.121189, Institutional Repository
Reynaert, E., Nagappa, D., Sigrist, J. A., & Morgenroth, E. (2024). Ensuring microbial water quality for on-site water reuse: importance of online sensors for reliable operation. Water Research X, 22, 100215 (8 pp.). doi:10.1016/j.wroa.2024.100215, Institutional Repository
Ruan, C., Ramoneda, J., Kan, A., Rudge, T. J., Wang, G., & Johnson, D. R. (2024). Phage predation accelerates the spread of plasmid-encoded antibiotic resistance. Nature Communications, 15, 5397 (12 pp.). doi:10.1038/s41467-024-49840-7, Institutional Repository
Stancanelli, L. M., Secchi, E., & Holzner, M. (2024). Magnetic fluid film enables almost complete drag reduction across laminar and turbulent flow regimes. Communications Physics, 7, 30 (9 pp.). doi:10.1038/s42005-023-01509-1, Institutional Repository
Sylvestre, É., Jahne, M. A., Reynaert, E., Morgenroth, E., & Julian, T. R. (2024). A critical evaluation of parametric models for predicting faecal indicator bacteria concentrations in greywater. Microbial Risk Analysis, 26, 100297 (8 pp.). doi:10.1016/j.mran.2024.100297, Institutional Repository
Takahashi, K., Oshiki, M., Ruan, C., Morinaga, K., Toyofuku, M., Nomura, N., & Johnson, D. R. (2024). Denitrification in low oxic environments increases the accumulation of nitrogen oxide intermediates and modulates the evolutionary potential of microbial populations. Environmental Microbiology Reports, 16(1), e13221 (14 pp.). doi:10.1111/1758-2229.13221, Institutional Repository
Tang, L., Rhoads, W. J., Eichelberg, A., Hamilton, K. A., & Julian, T. R. (2024). Applications of quantitative microbial risk assessment to respiratory pathogens and implications for uptake in policy: a state-of-the-science review. Environmental Health Perspectives, 132(5), 56001 (16 pp.). doi:10.1289/EHP12695, Institutional Repository
Ugolini, G. S., Wang, M., Secchi, E., Pioli, R., Ackermann, M., & Stocker, R. (2024). Microfluidic approaches in microbial ecology. Lab on a Chip, 24, 1394-1418. doi:10.1039/d3lc00784g, Institutional Repository
Wang, M., Chen, X., Fang, Y., Zheng, X., Huang, T., Nie, Y., & Wu, X. L. (2024). The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities. Cell Systems, 15(1), 63-74.e5. doi:10.1016/j.cels.2023.12.004, Institutional Repository
Wu, F., Yuan, C., Ruan, C., Zheng, M., Liu, L., Wang, G., & Chen, G. (2024). Coagulation promotes the spread of antibiotic resistance genes in secondary effluents. Environmental Pollution, 355, 124245 (10 pp.). doi:10.1016/j.envpol.2024.124245, Institutional Repository
Yu, Y., Trottmann, N. F., Schärer, M. R., Fenner, K., & Robinson, S. L. (2024). Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater. Water Research, 256, 121593 (9 pp.). doi:10.1016/j.watres.2024.121593, Institutional Repository
Zeugin, T., Coulter, F. B., Gülan, U., Studart, A. R., & Holzner, M. (2024). In vitro investigation of the blood flow downstream of a 3D-printed aortic valve. Scientific Reports, 14, 1572 (12 pp.). doi:10.1038/s41598-024-51676-6, Institutional Repository


Aligolzadeh, F., Holzner, M., & Dawson, J. R. (2023). Entrainment, detrainment and enstrophy transport by small-scale vortex structures. Journal of Fluid Mechanics, 973, A5 (23 pp.). doi:10.1017/jfm.2023.745, Institutional Repository
Brizzolara, S., Mollicone, J. P., van Reeuwijk, M., & Holzner, M. (2023). Entrainment at multi-scales in shear-dominated and Rayleigh-Taylor turbulence. European Journal of Mechanics: B/Fluids, 101, 294-302. doi:10.1016/j.euromechflu.2023.06.005, Institutional Repository
Burz, S. D., Causevic, S., Co, A. D., Dmitrijeva, M., Engel, P., Garrido-Sanz, D., … Vorholt, J. A. (2023). From microbiome composition to functional engineering, one step at a time. Microbiology and Molecular Biology Reviews, 87(4), 1-34. doi:10.1128/mmbr.00063-23, Institutional Repository
Cantrell, M. E., Sylvestre, É., Wharton, H. C., Scheidegger, R., Curchod, L., Gute, D. M., … Pickering, A. J. (2023). Hands are frequently contaminated with fecal bacteria and enteric pathogens globally: a systematic review and meta-analysis. ACS Environmental Au, 3(3), 123-134. doi:10.1021/acsenvironau.2c00039, Institutional Repository
Cavallaro, A., Rhoads, W. J., Sylvestre, É., Marti, T., Walser, J. C., & Hammes, F. (2023). Legionella relative abundance in shower hose biofilms is associated with specific microbiome members. FEMS Microbes, 4, xtad016 (13 pp.). doi:10.1093/femsmc/xtad016, Institutional Repository
Chen, X., Wang, M., Xing, Y., Nie, Y., & Wu, X. L. (2023). Assembly of microbial communities engaging in metabolic division of labor in a diffusion-limited environment is governed by metabolic flux. ACS Synthetic Biology, 12(7), 1972-1980. doi:10.1021/acssynbio.3c00022, Institutional Repository
Chen, G., Hu, Z., Ebrahimi, A., Johnson, D. R., Wu, F., Sun, Y., … Wang, G. (2023). Chemotactic movement and zeta potential dominate Chlamydomonas microsphaera attachment and biocathode development. Environmental Technology, 44(12), 1838-1849. doi:10.1080/09593330.2021.2014575, Institutional Repository
D'Souza, G., Schwartzman, J., Keegstra, J., Schreier, J. E., Daniels, M., Cordero, O. X., … Ackermann, M. (2023). Interspecies interactions determine growth dynamics of biopolymer-degrading populations in microbial communities. Proceedings of the National Academy of Sciences of the United States of America PNAS, 120(44), e2305198120 (9 pp.). doi:10.1073/pnas.2305198120, Institutional Repository
Daniels, M., van Vliet, S., & Ackermann, M. (2023). Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community. ISME Journal, 17(3), 406-416. doi:10.1038/s41396-022-01312-w, Institutional Repository
Dowdell, K. S., Healy, H. G., Joshi, S., Grimard-Conea, M., Pitell, S., Song, Y., … Rhoads, W. J. (2023). Legionella pneumophila occurrence in reduced-occupancy buildings in 11 cities during the COVID-19 pandemic. Environmental Science: Water Research and Technology, 9(11), 2847-2865. doi:10.1039/d3ew00278k, Institutional Repository
D’Souza, G., Ebrahimi, A., Stubbusch, A., Daniels, M., Keegstra, J., Stocker, R., … Ackermann, M. (2023). Cell aggregation is associated with enzyme secretion strategies in marine polysaccharide-degrading bacteria. ISME Journal, 17, 703-711. doi:10.1038/s41396-023-01385-1, Institutional Repository
Feng, M., Varliero, G., Qi, W., Stierli, B., Edwards, A., Robinson, S., … Frey, B. (2023). Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environmental Microbiology, 25(12), 3116-3138. doi:10.1111/1462-2920.16497, Institutional Repository
Fink, J. W., & Manhart, M. (2023). How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution. Current Opinion in Systems Biology, 36, 100470 (11 pp.). doi:10.1016/j.coisb.2023.100470, Institutional Repository
Fink, J. W., Held, N. A., & Manhart, M. (2023). Microbial population dynamics decouple growth response from environmental nutrient concentration. Proceedings of the National Academy of Sciences of the United States of America PNAS, 120(2), e2207295120 (11 pp.). doi:10.1073/pnas.2207295120, Institutional Repository
Fischer, F. B., Bigler, M., Mäusezahl, D., Hattendorf, J., Egli, A., Julian, T. R., … Wiggli, B. (2023). Legionnaires' disease in Switzerland: rationale and study protocol of a prospective national case–control and molecular source attribution study (SwissLEGIO). Infection, 51, 1467-1479. doi:10.1007/s15010-023-02014-x, Institutional Repository
Ge, Z. B., Zhai, Z. Q., Xie, W. Y., Dai, J., Huang, K., Johnson, D. R., … Wang, P. (2023). Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria. ISME Journal, 17, 2090-2102. doi:10.1038/s41396-023-01519-5, Institutional Repository
Han, M., Niu, X., Xiong, G., Ruan, C., Chen, G., Wu, H., … Wang, G. (2023). Isolation, characterization and genomic analysis of the novel Arthrobacter sp. phage SWEP2. Archives of Virology, 168(11), 276 (5 pp.). doi:10.1007/s00705-023-05898-0, Institutional Repository
Hockenberry, A., Slack, E., & Stadtmueller, B. M. (2023). License to clump: secretory IgA structure-function relationships across scales. Annual Review of Microbiology, 77, 645-668. doi:10.1146/annurev-micro-032521-041803, Institutional Repository
Huanambal-Sovero, V. A., Abkar, L., Ovie, E. S., Colangelo, T., Julian, T. R., & Beck, S. E. (2023). Permeate microbiome reflects the biofilm microbial community in a gravity-driven woven-fiber microfiltration (WFMF) system for wastewater treatment. Environmental Science: Water Research and Technology, 9, 2605-2618. doi:10.1039/d3ew00200d, Institutional Repository
Karakurt-Fischer, S., Johnson, D. R., Fenner, K., & Hafner, J. (2023). Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia. Water Research, 247, 120756 (7 pp.). doi:10.1016/j.watres.2023.120756, Institutional Repository
Keshaviah, A., Diamond, M. B., Wade, M. J., Scarpino, S. V., Ahmed, W., Amman, F., … Ort, C. (2023). Wastewater monitoring can anchor global disease surveillance systems. Lancet Global Health, 11(6), e976-e981. doi:10.1016/S2214-109X(23)00170-5, Institutional Repository
Kliesmete, Z., Wange, L. E., Vieth, B., Esgleas, M., Radmer, J., Hülsmann, M., … Enard, W. (2023). Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals. eLife, 12, e83593 (29 pp.). doi:10.7554/elife.83593, Institutional Repository
Li, C., Sylvestre, É., Fernandez-Cassi, X., Julian, T. R., & Kohn, T. (2023). Waterborne virus transport and the associated risks in a large lake. Water Research, 229, 119437 (14 pp.). doi:10.1016/j.watres.2022.119437, Institutional Repository
Luo, N., Wang, M., Nie, Y., & Wu, X. L. (2023). Volatile compounds-induced environmental pH shifts mediate interspecific bacterial interactions over long-distance. Science of the Total Environment, 892, 164577 (10 pp.). doi:10.1016/j.scitotenv.2023.164577, Institutional Repository
Ma, Y., Ramoneda, J., & Johnson, D. R. (2023). Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion. Nature Communications, 14(1), 3530 (12 pp.). doi:10.1038/s41467-023-39354-z, Institutional Repository
Markale, I., Carrel, M., Kurz, D. L., Morales, V. L., Holzner, M., & Jiménez-Martínez, J. (2023). Internal biofilm heterogeneities enhance solute mixing and chemical reactions in porous media. Environmental Science and Technology, 57(21), 8065-8074. doi:10.1021/acs.est.2c09082, Institutional Repository
Marti, T. D., Schärer, M. R., & Robinson, S. L. (2023). Microbial biocatalysis within us: the underexplored xenobiotic biotransformation potential of the urinary tract microbiota. Chimia, 77(6), 424-431. doi:10.2533/chimia.2023.424, Institutional Repository
Micali, G., Hockenberry, A. M., Dal Co, A., & Ackermann, M. (2023). Minorities drive growth resumption in cross-feeding microbial communities. Proceedings of the National Academy of Sciences of the United States of America PNAS, 120(45), e2301398120 (9 pp.). doi:10.1073/pnas.2301398120, Institutional Repository
Mullowney, M. W., Duncan, K. R., Elsayed, S. S., Garg, N., van der Hooft, J. J. J., Martin, N. I., … Medema, M. H. (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery, 22, 895-916. doi:10.1038/s41573-023-00774-7, Institutional Repository
Raes, B., Wang, J., Horemans, B., Dirckx, L., Waldherr, S., Kohler, H. P. E., & Springael, D. (2023). The growth yield of Aminobacter niigataensis MSH1 on the micropollutant 2,6-Dichlorobenzamide decreases substantially at trace substrate concentrations. Environmental Science and Technology, 58, 2859-2869. doi:10.1021/acs.est.3c06883, Institutional Repository
Reynaert, E., Gretener, F., Julian, T. R., & Morgenroth, E. (2023). Sensor setpoints that ensure compliance with microbial water quality targets for membrane bioreactor and chlorination treatment in on-site water reuse systems. Water Research X, 18, 100164 (13 pp.). doi:10.1016/j.wroa.2022.100164, Institutional Repository
Robinson, S. L. (2023). Structure-guided metagenome mining to tap microbial functional diversity. Current Opinion in Microbiology, 76, 102382 (6 pp.). doi:10.1016/j.mib.2023.102382, Institutional Repository
Ruan, C., Borer, B., Ramoneda, J., Wang, G., & Johnson, D. R. (2023). Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth. npj Biofilms and Microbiomes, 9, 58 (10 pp.). doi:10.1038/s41522-023-00428-x, Institutional Repository
Schmid, S., Jeevannavar, A., Julian, T. R., & Tamminen, M. (2023). Portable BLAST-like algorithm library and its implementations for command line, Python, and R. PLoS One, 18(11), e0289693 (5 pp.). doi:10.1371/journal.pone.0289693, Institutional Repository
Shnapp, R., Brizzolara, S., Neamtu-Halic, M. M., Gambino, A., & Holzner, M. (2023). Universal alignment in turbulent pair dispersion. Nature Communications, 14(1), 4195 (9 pp.). doi:10.1038/s41467-023-39903-6, Institutional Repository
Sylvestre, É., Reynaert, E., & Julian, T. R. (2023). Defining risk-based monitoring frequencies to verify the performance of water treatment barriers. Environmental Science and Technology Letters, 10(4), 374-384. doi:10.1021/acs.estlett.3c00154, Institutional Repository
Terlouw, B. R., Blin, K., Navarro-Muñoz, J. C., Avalon, N. E., Chevrette, M. G., Egbert, S., … Medema, M. H. (2023). MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Research, 51(D1), D603-D610. doi:10.1093/nar/gkac1049, Institutional Repository
Wang, Y., Ruan, C., Xie, W., Zhu, K., Chen, G., Liu, Y., & Wang, G. (2023). Effects of microscopic water and nutrient conditions on the host lysis process of pseudomonas aeruginosa phage. Tu Rang Xue Bao/Acta Pedologica Sinica, 60(3), 835-845. doi:10.11766/trxb202201070528, Institutional Repository
Wichmann, N., Gruseck, R., & Zumstein, M. (2023). Hydrolysis of antimicrobial peptides by extracellular peptidases in wastewater. Environmental Science and Technology, 58(1), 717-726. doi:10.1021/acs.est.3c06506, Institutional Repository
Wu, H., Wan, S., Ruan, C., Wan, W., Han, M., Chen, G., … Wang, G. (2023). Soil microbial necromass: the state-of-the-art, knowledge gaps, and future perspectives. European Journal of Soil Biology, 115, 103472 (11 pp.). doi:10.1016/j.ejsobi.2023.103472, Institutional Repository
Ziliani, A., Bovio-Winkler, P., Cabezas, A., Etchebehere, C., Garcia, H. A., López-Vázquez, C. M., … Rubio-Rincón, F. J. (2023). Putative metabolism of Ca. Accumulibacter via the utilization of glucose. Water Research, 229, 119446 (14 pp.). doi:10.1016/j.watres.2022.119446, Institutional Repository
van Gestel, J., Wagner, A., & Ackermann, M. (2023). Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biology, 21(10), e3002338 (22 pp.). doi:10.1371/journal.pbio.3002338, Institutional Repository


Dolinšek, J., Ramoneda, J., & Johnson, D. R. (2022). Initial community composition determines the long-term dynamics of a microbial cross-feeding interaction by modulating niche availability. ISME Communications, 2(1), 77 (10 pp.). doi:10.1038/s43705-022-00160-1, Institutional Repository
Scott, T. A., Verest, M., Farnung, J., Forneris, C. C., Robinson, S. L., Ji, X., … Piel, J. (2022). Widespread microbial utilization of ribosomal β-amino acid-containing peptides and proteins. Chem, 8(10), 2659-2677. doi:10.1016/j.chempr.2022.09.017, Institutional Repository
Julian, T. R., Fernandez, X., Ort, C., & Kahn, T. (2022). How wastewater informs COVID-19 policy in Switzerland. Water Science Policy (3 pp.). doi:10.53014/BHET9151, Institutional Repository
Fraley, A. E., Robinson, S. L., & Piel, J. (2022). The versatile natural product enzymology of marine microbial communities. Aldrichimica Acta, 55(3), 55-75. , Institutional Repository
Ruan, C., Xiong, G., Niu, X., Chen, G., Wu, H., Ma, Z., … Wang, G. (2022). Preliminary analysis of the virus metagenome in a farmland black soil of Northeast China. Tu Rang Xue Bao/Acta Pedologica Sinica, 59(5), 1447-1456. doi:10.11766/trxb202104230215, Institutional Repository
Wang, M., Chen, X., Tang, Y. Q., Nie, Y., & Wu, X. L. (2022). Substrate availability and toxicity shape the structure of microbial communities engaged in metabolic division of labor. mLife, 1(2), 131-145. doi:10.1002/mlf2.12025, Institutional Repository
Hu, H., Wang, M., Huang, Y., Xu, Z., Xu, P., Nie, Y., & Tang, H. (2022). Guided by the principles of microbiome engineering: accomplishments and perspectives for environmental use. mLife, 1(4), 382-398. doi:10.1002/mlf2.12043, Institutional Repository
Van Riet, S., Tadesse, W., Mortier, J., Schlegel, S., Simoens, K., Bernaerts, K., … Aertsen, A. (2022). Heterogeneity and evolutionary tunability of Escherichia coli resistance against extreme acid stress. Microbiology Spectrum, 10(6), 1-13. doi:10.1128/spectrum.03757-22, Institutional Repository
Amin, M. B., Talukdar, P. K., Asaduzzaman, M., Roy, S., Flatgard, B. M., Islam, M. R., … Islam, M. A. (2022). Effects of chronic exposure to arsenic on the fecal carriage of antibiotic-resistant Escherichia coli among people in rural Bangladesh. PLoS Pathogens, 18(12), e1010952 (23 pp.). doi:10.1371/journal.ppat.1010952, Institutional Repository
Povolo, V. R. (2022). Causes and consequences of group formation during the degradation of carbon polymers by bacteria (Doctoral dissertation). ETH Zurich, Zurich, 165 p. , Institutional Repository
Montealegre, M. C., Greenwood, E. E., Teichmann, L., Nadimpalli, M. L., Caduff, L., Swarthout, J. M., … Julian, T. R. (2022). Drinking water chlorination impact on fecal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae in Bangladeshi children in a double-blind, cluster-randomized controlled trial. Environmental Health Perspectives, 130(11), 117702 (3 pp.). doi:10.1289/EHP11359, Institutional Repository
George, C. M., Birindwa, A., Beck, S., Julian, T. R., Kuhl, J., Williams, C., … Cirhuza, L. B. (2022). Fecal contamination in child play spaces and on child hands are associated with subsequent adverse child developmental outcomes in rural Democratic Republic of the Congo: REDUCE prospective cohort study. American Journal of Tropical Medicine and Hygiene, 106(4), 1141-1148. doi:10.4269/ajtmh.21-0706, Institutional Repository
Ruan, C., Ramoneda, J., Gogia, G., Wang, G., & Johnson, D. R. (2022). Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion. Current Biology, 32(24), 5285-5294. doi:10.1016/j.cub.2022.11.009, Institutional Repository
Paoli, L., Robinson, S., & Moore, B. (2022). A wealth of new biosynthetic pathways from the global ocean microbiome. Nature (2 pp.). doi:10.1038/d41586-022-01545-x, Institutional Repository
Schubert, O. T., Bloom, J. S., Sadhu, M. J., & Kruglyak, L. (2022). Genome-wide base editor screen identifies regulators of protein abundance in yeast. eLife, 11, e79525 (29 pp.). doi:10.7554/eLife.79525, Institutional Repository
Huelsmann, M., & Ackermann, M. (2022). Community instability in the microbial world. Science, 378(6615), 29-30. doi:10.1126/science.ade2516, Institutional Repository
Cariti, F., Tuñas Corzon, A., Fernandez-Cassi, X., Ganesanandamoorthy, P., Ort, C., Julian, T. R., & Kohn, T. (2022). Wastewater reveals the spatiotemporal spread of SARS-CoV-2 in the Canton of Ticino (Switzerland) during the onset of the COVID-19 pandemic. ACS ES&T Water, 2(11), 2194-2200. doi:10.1021/acsestwater.2c00082, Institutional Repository
Nelson, T. F., Baumgartner, R., Jaggi, M., Bernasconi, S. M., Battagliarin, G., Sinkel, C., … Sander, M. (2022). Biodegradation of poly(butylene succinate) in soil laboratory incubations assessed by stable carbon isotope labelling. Nature Communications, 13(1), 5691 (16 pp.). doi:10.1038/s41467-022-33064-8, Institutional Repository
Wang, M., Chen, X., Liu, X., Fang, Y., Zheng, X., Huang, T., … Wu, X. L. (2022). Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor. Cell Reports, 40(13), 111410 (20 pp.). doi:10.1016/j.celrep.2022.111410, Institutional Repository
Wu, H., Wan, S., Ruan, C., Niu, X., Chen, G., Liu, Y., … Wang, G. (2022). Phage-bacterium interactions and nutrient availability can shape C and N retention in microbial biomass. European Journal of Soil Science, 73(4), e13296 (5 pp.). doi:10.1111/ejss.13296, Institutional Repository
Cavallaro, A., Rhoads, W. J., Huwiler, S. G., Stachler, E., & Hammes, F. (2022). Potential probiotic approaches to control Legionella in engineered aquatic ecosystems. FEMS Microbiology Ecology, 98(8), 1-9. doi:10.1093/femsec/fiac071, Institutional Repository
Jahn, K., Dreifuss, D., Topolsky, I., Kull, A., Ganesanandamoorthy, P., Fernandez-Cassi, X., … Beerenwinkel, N. (2022). Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC. Nature Microbiology, 7, 1151-1160. doi:10.1038/s41564-022-01185-x, Institutional Repository
Schwartzman, J. A., Ebrahimi, A., Chadwick, G., Sato, Y., Roller, B. R. K., Orphan, V. J., & Cordero, O. X. (2022). Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. Current Biology, 32(14), 3059-3069.e7. doi:10.1016/j.cub.2022.06.011, Institutional Repository
Conforti, S., & Costantini, F. (2022). Potential crypticity within two decapod (Crustacea) genera: Galathea Fabricius, 1793 and Eualus Thallwitz, 1891 suggested by integrative taxonomic approach. Mediterranean Marine Science, 23(3), 499-524. doi:10.12681/mms.27733, Institutional Repository
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Montealegre, M. C., Roy, S., Böni, F., Hossain, M. I., Navab-Daneshmand, T., Caduff, L., … Julian, T. R. (2018). Risk factors for detection, survival, and growth of antibiotic-resistant and pathogenic Escherichia coli in household soils in rural Bangladesh. Applied and Environmental Microbiology, 84(24), e01978-18 (14 pp.). doi:10.1128/AEM.01978-18, Institutional Repository
Navab-Daneshmand, T., Friedrich, M. N. D., Gächter, M., Montealegre, M. C., Mlambo, L. S., Nhiwatiwa, T., … Julian, T. R. (2018). Escherichia coli contamination across multiple environmental compartments (soil, hands, drinking water, and handwashing water) in urban Harare: correlations and risk factors. American Journal of Tropical Medicine and Hygiene, 98(3), 803-813. doi:10.4269/ajtmh.17-0521, Institutional Repository
Nescerecka, A., Juhna, T., & Hammes, F. (2018). Identifying the underlying causes of biological instability in a full-scale drinking water supply system. Water Research, 135, 11-21. doi:10.1016/j.watres.2018.02.006, Institutional Repository
Neu, L., Proctor, C. R., & Hammes, F. (2018). Der finale Meter. Biofilme in Duschschläuchen. Aqua & Gas, 98(5), 42-45. , Institutional Repository
Neu, L., Bänziger, C., Proctor, C. R., Zhang, Y., Liu, W. T., & Hammes, F. (2018). Ugly ducklings - the dark side of plastic materials in contact with potable water. npj Biofilms and Microbiomes, 4(1), 7 (11 pp.). doi:10.1038/s41522-018-0050-9, Institutional Repository
Oh, S., Hammes, F., & Liu, W. T. (2018). Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant. Water Research, 128, 278-285. doi:10.1016/j.watres.2017.10.054, Institutional Repository
Patsch, D., van Vliet, S., Garbani Marcantini, L., & Johnson, D. R. (2018). Generality of associations between biological richness and the rates of metabolic processes across microbial communities. Environmental Microbiology, 20(12), 4356-4368. doi:10.1111/1462-2920.14352, Institutional Repository
Pitol, A. K., Bischel, H. N., Boehm, A. B., Kohn, T., & Julian, T. R. (2018). Transfer of enteric viruses adenovirus and coxsackievirus and bacteriophage MS2 from liquid to human skin. Applied and Environmental Microbiology, 84(22), e01809-18 (13 pp.). doi:10.1128/AEM.01809-18, Institutional Repository
Prest, E. I., Schaap, P. G., & Hammes, F. (2018). Analyse microbiologique en ligne. Étude des variations de la qualité microbiologique de l'eau potable dans une usine de traitement. Aqua & Gas, 98(5), 20-24. , Institutional Repository
Proctor, C. R., Reimann, M., Vriens, B., & Hammes, F. (2018). Biofilms in shower hoses. Water Research, 131, 274-286. doi:10.1016/j.watres.2017.12.027, Institutional Repository
Proctor, C. R., Besmer, M. D., Langenegger, T., Beck, K., Walser, J. C., Ackermann, M., … Hammes, F. (2018). Phylogenetic clustering of small low nucleic acid-content bacteria across diverse freshwater ecosystems. ISME Journal, 12, 1344-1359. doi:10.1038/s41396-018-0070-8, Institutional Repository
Props, R., Rubbens, P., Besmer, M., Buysschaert, B., Sigrist, J., Weilenmann, H., … Hammes, F. (2018). Detection of microbial disturbances in a drinking water microbial community through continuous acquisition and advanced analysis of flow cytometry data. Water Research, 145, 73-82. doi:10.1016/j.watres.2018.08.013, Institutional Repository
Rotem, A., Serohijos, A. W. R., Chang, C. B., Wolfe, J. T., Fischer, A. E., Mehoke, T. S., … Shakhnovich, E. I. (2018). Evolution on the biophysical fitness landscape of an RNA virus. Molecular Biology and Evolution, 35(10), 2390-2400. doi:10.1093/molbev/msy131, Institutional Repository
Savio, D., Stadler, P., Reischer, G. H., Kirschner, A. K. T., Demeter, K., Linke, R., … Farnleitner, A. H. (2018). Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management. Wiley Interdisciplinary Reviews: Water, 5(3), e1282 (20 pp.). doi:10.1002/wat2.1282, Institutional Repository
Shettigar, M., Balotra, S., Cahill, D., Warden, A. C., Lacey, M. J., Kohler, H. P. E., … Pandey, G. (2018). Isolation of the (+)-pinoresinol-mineralizing Pseudomonas sp. strain SG-MS2 and elucidation of its catabolic pathway. Applied and Environmental Microbiology, 84(4), e02531-17 (14 pp.). doi:10.1128/AEM.02531-17, Institutional Repository
Sun, L., Alexander, H. K., Bogos, B., Kiviet, D. J., Ackermann, M., & Bonhoeffer, S. (2018). Effective polyploidy causes phenotypic delay and influences bacterial evolvability. PLoS Biology, 16(2), e2004644 (24 pp.). doi:10.1371/journal.pbio.2004644, Institutional Repository
T'Syen, J., Raes, B., Horemans, B., Tassoni, R., Leroy, B., Lood, C., … Springael, D. (2018). Catabolism of the groundwater micropollutant 2,6-dichlorobenzamide beyond 2,6-dichlorobenzoate is plasmid encoded in Aminobacter sp. MSH1. Applied Microbiology and Biotechnology, 102(18), 7963-7979. doi:10.1007/s00253-018-9189-9, Institutional Repository
Vignola, M., Werner, D., Hammes, F., King, L. C., & Davenport, R. J. (2018). Flow-cytometric quantification of microbial cells on sand from water biofilters. Water Research, 143, 66-76. doi:10.1016/j.watres.2018.05.053, Institutional Repository
Vulin, C., Leimer, N., Huemer, M., Ackermann, M., & Zinkernagel, A. S. (2018). Prolonged bacterial lag time results in small colony variants that represent a sub-population of persisters. Nature Communications, 9(1), 4074 (8 pp.). doi:10.1038/s41467-018-06527-0, Institutional Repository
Zimmermann, M., Escrig, S., Lavik, G., Kuypers, M. M. M., Meibom, A., Ackermann, M., & Schreiber, F. (2018). Substrate and electron donor limitation induce phenotypic heterogeneity in different metabolic activities in a green sulphur bacterium. Environmental Microbiology Reports, 10(2), 179-183. doi:10.1111/1758-2229.12616, Institutional Repository
Zumstein, M. T., Schintlmeister, A., Nelson, T. F., Baumgartner, R., Woebken, D., Wagner, M., … Sander, M. (2018). Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass. Science Advances, 4(7), eaas9024 (8 pp.). doi:10.1126/sciadv.aas9024, Institutional Repository
van Vliet, S., Dal Co, A., Winkler, A. R., Spriewald, S., Stecher, B., & Ackermann, M. (2018). Spatially correlated gene expression in bacterial groups: the role of lineage history, spatial gradients, and cell-cell interactions. Cell Systems, 6(4), 496-507. doi:10.1016/j.cels.2018.03.009, Institutional Repository


Ackermann, M., & van Vliet, S. (2017). Stochastic gene expression: bacterial elites in chemotaxis. Molecular Systems Biology, 13(1), 909-910. doi:10.15252/msb.20167458, Institutional Repository
Bayramoglu, B., Toubiana, D., van Vliet, S., Inglis, R. F., Shnerb, N., & Gillor, O. (2017). Bet-hedging in bacteriocin producing Escherichia coli populations: the single cell perspective. Scientific Reports, 7, 1-10. doi:10.1038/srep42068, Institutional Repository
Bergmiller, T., Andersson, A. M. C., Tomasek, K., Balleza, E., Kiviet, D. J., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Science, 356(6335), 311-315. doi:10.1126/science.aaf4762, Institutional Repository
Besmer, M. D., Hammes, F., Sigrist, J. A., & Ort, C. (2017). Evaluating monitoring strategies to detect precipitation-induced microbial contamination events in karstic springs used for drinking water. Frontiers in Microbiology, 8, 2229 (12 pp.). doi:10.3389/fmicb.2017.02229, Institutional Repository
Besmer, M. D., Sigrist, J. A., Props, R., Buysschaert, B., Mao, G., Boon, N., & Hammes, F. (2017). Laboratory-scale simulation and real-time tracking of a microbial contamination event and subsequent shock-chlorination in drinking water. Frontiers in Microbiology, 8, 1900 (11 pp.). doi:10.3389/fmicb.2017.01900, Institutional Repository
Bosshard, L., Dupanloup, I., Tenaillon, O., Bruggmann, R., Ackermann, M., Peischl, S., & Excoffier, L. (2017). Accumulation of deleterious mutations during bacterial range expansions. Genetics, 207(2), 669-684. doi:10.1534/genetics.117.300144, Institutional Repository
Böhler, M., Fleiner, J., Siegrist, H., McArdell, C. S., Teichler, R., Bourgin, M., … Blunschi, M. (2017). Biologische Nachbehandlung von kommunalem Abwasser nach Ozonung – ReTREAT. Schlussbericht. Dübendorf: Eawag. , Institutional Repository
Casotti, R., Balestra, C., Van Dijk, M., Passarelli, A., Sigrist, J., & Hammes, F. (2017). Real-time microbial concentrations by automated on-line flow cytometry for marine coastal monitoring. In IMEKO TC19 workshop on metrology for the sea (MetroSea 2017). Learning to measure sea health parameters (pp. 50-53). Budapest: International Measurement Confederation (IMEKO). , Institutional Repository
Diard, M., Bakkeren, E., Cornuault, J. K., Moor, K., Hausmann, A., Sellin, M. E., … Hardt, W. D. (2017). Inflammation boosts bacteriophage transfer between Salmonella spp.. Science, 355(6330), 1211-1215. doi:10.1126/science.aaf8451, Institutional Repository
Epting, J., Huggenberger, P., Page, R. M., Besmer, M. D., Hammes, F., Radny, D., … Borer, P. (2017). Variabilität der grundwasserqualität. Einflussfaktoren für die Grundwasserqualität Flussnaher Trinkwasserfassungen. Aqua & Gas, 97(2), 30-39. , Institutional Repository
Friedrich, M. N. D., Julian, T. R., Kappeler, A., Nhiwatiwa, T., & Mosler, H. J. (2017). Handwashing, but how? Microbial effectiveness of existing handwashing practices in high-density suburbs of Harare, Zimbabwe. American Journal of Infection Control, 45(3), 228-233. doi:10.1016/j.ajic.2016.06.035, Institutional Repository
Goldschmidt, F., Regoes, R. R., & Johnson, D. R. (2017). Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations. ISME Journal, 11(9), 2112-2123. doi:10.1038/ismej.2017.76, Institutional Repository
González-González, A., Hug, S. M., Rodríguez-Verdugo, A., Patel, J. S., & Gaut, B. S. (2017). Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression. Molecular Biology and Evolution, 34(11), 2839-2855. doi:10.1093/molbev/msx216, Institutional Repository
Heeb, N. V., Grubelnik, A., Geueke, B., Kohler, H. P. E., & Lienemann, P. (2017). Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26. Chemosphere, 182, 491-500. doi:10.1016/j.chemosphere.2017.05.047, Institutional Repository
König, B., Bochet, C., Egli, T., Kling, S., Norton, B., & Wehrli, B. (2017). Uses of daylight. In S. Sanders & J. Oberst (Eds.), Changing perspectives on daylight: science, technology, and culture (pp. 38-42). Retrieved from http://www.sciencemag.org/collections/changing-perspectives-daylight-science-technology-and-culture, Institutional Repository
Kötzsch, S., Rölli, F., & Hammes, F. (2017). Trinkwasserqualität in Gebäuden. Synthesebericht: KTI-Projekt «Materialien in Kontakt mit Trinkwasser». Aqua & Gas, 97(10), 74-78. , Institutional Repository
Lilja, E. E., & Johnson, D. R. (2017). Metabolite toxicity determines the pace of molecular evolution within microbial populations. BMC Evolutionary Biology, 17, 52 (12 pp.). doi:10.1186/s12862-017-0906-2, Institutional Repository
Marchal, M., Goldschmidt, F., Derksen-Müller, S. N., Panke, S., Ackermann, M., & Johnson, D. R. (2017). A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations. BMC Evolutionary Biology, 17, 106 (14 pp.). doi:10.1186/s12862-017-0950-y, Institutional Repository
Mathis, R., & Ackermann, M. (2017). Asymmetric cellular memory in bacteria exposed to antibiotics. BMC Evolutionary Biology, 17, 73 (14 pp.). doi:10.1186/s12862-017-0884-4, Institutional Repository
Men, Y., Achermann, S., Helbling, D. E., Johnson, D. R., & Fenner, K. (2017). Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation. Water Research, 109, 217-226. doi:10.1016/j.watres.2016.11.048, Institutional Repository
Micali, G., Colin, R., Sourjik, V., & Endres, R. G. (2017). Drift and behavior of E. coli cells. Biophysical Journal, 113(11), 2321-2325. doi:10.1016/j.bpj.2017.09.031, Institutional Repository
Montealegre, M. C., Roh, J. H., Rae, M., Davlieva, M. G., Singh, K. V., Shamoo, Y., & Murray, B. E. (2017). Differential Penicillin-Binding Protein 5 (PBP5) levels in the Enterococcus faecium clades with different levels of ampicillin resistance. Antimicrobial Agents and Chemotherapy, 61(1), e02034 (10 pp.). doi:10.1128/AAC.02034-16, Institutional Repository
Moor, K., Diard, M., Sellin, M. E., Felmy, B., Wotzka, S. Y., Toska, A., … Slack, E. (2017). High-avidity IgA protects the intestine by enchaining growing bacteria. Nature, 544(7651), 498-502. doi:10.1038/nature22058, Institutional Repository
Nguyen, M. T., Allemann, L., Ziemba, C., Larivé, O., Morgenroth, E., & Julian, T. R. (2017). Controlling bacterial pathogens in water for reuse: treatment technologies for water recirculation in the Blue Diversion Autarky Toilet. Frontiers in Environmental Science, 5, 90 (13 pp.). doi:10.3389/fenvs.2017.00090, Institutional Repository
Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D. J., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics, 13(12), e1007122 (24 pp.). doi:10.1371/journal.pgen.1007122, Institutional Repository
Page, R. M., Besmer, M. D., Epting, J., Sigrist, J. A., Hammes, F., & Huggenberger, P. (2017). Online analysis: deeper insights into water quality dynamics in spring water. Science of the Total Environment, 599-600, 227-236. doi:10.1016/j.scitotenv.2017.04.204, Institutional Repository
Pati, S. G., Kohler, H. P. E., & Hofstetter, T. B. (2017). Characterization of substrate, cosubstrate, and product isotope effects associated with enzymatic oxygenations of organic compounds based on compound-specific isotope analysis. In M. E. Harris & V. E. Anderson (Eds.), Methods in enzymology: Vol. 596. Measurement and analysis of kinetic isotope effects (pp. 291-329). doi:10.1016/bs.mie.2017.06.044, Institutional Repository
Pitol, A. K., Bischel, H. N., Kohn, T., & Julian, T. R. (2017). Virus transfer at the skin−liquid interface. Environmental Science and Technology, 51, 14417-14425. doi:10.1021/acs.est.7b04949, Institutional Repository
Probst-Rüd, S., McNeill, K., & Ackermann, M. (2017). Thiouridine residues in tRNAs are responsible for a synergistic effect of UVA and UVB light in photoinactivation of Escherichia coli. Environmental Microbiology, 19(2), 434-442. doi:10.1111/1462-2920.13319, Institutional Repository
Proctor, C. R., Dai, D., Edwards, M. A., & Pruden, A. (2017). Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems. Microbiome, 5, 130-146. doi:10.1186/s40168-017-0348-5, Institutional Repository
Proctor, C. R. (2017). Microbiology of household plumbing causes and consequences (Doctoral dissertation). doi:10.3929/ethz-b-000255592, Institutional Repository
Props, R., Kerckhof, F. M., Rubbens, P., De Vrieze, J., Hernandez Sanabria, E., Waegeman, W., … Boon, N. (2017). Absolute quantification of microbial taxon abundances. ISME Journal, 11(587), 584-587. doi:10.1038/ismej.2016.117, Institutional Repository
Ricken, B., Kolvenbach, B. A., Bergesch, C., Benndorf, D., Kroll, K., Strnad, H., … Corvini, P. F. X. (2017). FMNH2-dependent monooxygenases initiate catabolism of sulfonamides in Microbacterium sp strain BR1 subsisting on sulfonamide antibiotics. Scientific Reports, 7, 15783 (11 pp.). doi:10.1038/s41598-017-16132-8, Institutional Repository
Rodriguez-Verdugo, A., Buckley, J., & Stapley, J. (2017). The genomic basis of eco-evolutionary dynamics. Molecular Ecology, 26(6), 1456-1464. doi:10.1111/mec.14045, Institutional Repository
Schiessl, K. T., Janssen, E. M. L., Kraemer, S. M., McNeill, K., & Ackermann, M. (2017). Magnitude and mechanism of siderophore-mediated competition at low iron solubility in the Pseudomonas aeruginosa pyochelin system. Frontiers in Microbiology, 8, 1964 (11 pp.). doi:10.3389/fmicb.2017.01964, Institutional Repository
Schiff, H. (2017). Development of a massively multiplexed ligation-dependent assay for antibiotic resistance gene detection (Master thesis). 70 p. , Institutional Repository
Shrivastava, N., Macwan, A. S., Kohler, H. P. E., & Kumar, A. (2017). Important amino acid residues of hexachlorocyclohexane dehydrochlorinases (LinA) for enantioselective transformation of hexachlorocyclohexane isomers. Biodegradation, 28(2-3), 171-180. doi:10.1007/s10532-017-9786-9, Institutional Repository
Van Nevel, S., Koetzsch, S., Proctor, C. R., Besmer, M. D., Prest, E. I., Vrouwenvelder, J. S., … Hammes, F. (2017). Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring. Water Research, 113, 191-206. doi:10.1016/j.watres.2017.01.065, Institutional Repository
Wells, G. F., Shi, Y., Laureni, M., Rosenthal, A., Szivák, I., Weissbrodt, D. G., … Morgenroth, E. (2017). Comparing the resistance, resilience, and stability of replicate moving bed biofilm and suspended growth combined nitritation–anammox reactors. Environmental Science and Technology, 51(9), 5108-5117. doi:10.1021/acs.est.6b05878, Institutional Repository