Publications

Stopnisek, Hedžet, Accetto. et al. Insights into Diversity, Host-Range, and Temporal Stability of Bacteroides and  Phocaeicola Prophages. BMC microbiology 25, 92 (2025). https://doi.org/10.1186/s12866-025-03827-6   

Rozman, Stopnisek, Mohar Lorbeg et al. Exploring the resistome of probiotics, starter cultures, and cheeses via metagenomic analysis. Food Control 175, 111173 (2025). https://doi.org/10.1016/j.foodcont.2025.111173

Valenzuela, J.J., Immanuel, S.R.C., Wilson, J. et al. Origin of biogeographically distinct ecotypes during laboratory evolution. Nature Communications 15, 7451 (2024). https://doi.org/10.1038/s41467-024-51759-y 

Guedes Stehling, E.,  Furlan, J.P.R, Lopes, R. et al. The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil. Environmental Pollution 348, 123849 (2024).  https://doi.org/10.1016/j.envpol.2024.123849

Sinha, R., LeVeque, R.M., Callahan, S.M.  et al. Gut Metabolite L-Lactate Supports Campylobacter Jejuni Population Expansion during Acute Infection. PNAS 121, e2316540120 (2024). https://doi.org/10.1073/pnas.2316540120

Sarango Flores, S., Cordovez, V., Oyserman, B. et al. The Tomato's Tale: Exploring Taxonomy, Biogeography, Domestication, and Microbiome for Enhanced Resilience. Phytobiomes Journal 8:1, 5-20 (2023). https://doi.org/10.1094/PBIOMES-09-23-0091-MF 

Howe, A., Stopnisek, N., Dooley, S.K. et al. Seasonal activities of the phyllosphere microbiome of perennial crops. Nature Communications 14, 1039 (2023). https://doi.org/10.1038/s41467-023-36515-y 

Oyserman, B., Sarango Flores, S., Griffioen, T. et al. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nature Communications 13, 3228 (2022). https://doi.org/10.1038/s41467-022-30849-9 

Bintarti, A.F., Sulesky-Grieb, A., Stopnisek, N. et al. Endophytic microbiome variation among single plant seeds. Phytobiomes Journal 6 (1), 45-55 (2022). https://doi.org/10.1094/PBIOMES-04-21-0030-R 

Syamsu Rizaludin, M., Stopnisek, N., Raaijmakers, J.M. et al. The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots. Metabolites; 11(6):357. https://doi.org/10.3390/metabo11060357

Stopnisek, N., Shade, A. Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. ISME Journal 15, 2708–2722. https://doi.org/10.1038/s41396-021-00955-5

Turkarslan, S., Stopnisek, N., Thompson, A.W. et al. Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions. ISME Journal 15, 2233–2247. https://doi.org/10.1038/s41396-021-00919-9

Hunt, K.A., Forbes, J. Taub, F. et al. An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates. Journal of Microbiological Methods; 188, 106294. https://doi.org/10.1016/j.mimet.2021.106294

Grady, K.L., Sorensen, J.W., Stopnisek, N., et al. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nature Communication 10, 4135. https://doi.org/10.1038/s41467-019-11974-4

Shade A., Stopnisek, N. Abundance-occupancy distributions to prioritize plant core microbiome membership. Current Opinion in Microbiology 49, 50-58. https://doi.org/10.1016/j.mib.2019.09.008

Bell, T.H., Hockett, K.L., Alcalá-Briseño, R.I. et al. Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities. Phytobiomes Journal 3:1, 3-21. https://doi.org/10.1094/PBIOMES-01-19-0006-W

Meinhardt, K.A., Stopnisek, N., Pannu, M.W. et al. Ammonia-oxidizing bacteria are the primary N2O producers in an ammonia-oxidizing archaea dominated alkaline agricultural soil. Environ Microbiol, 20: 2195-2206. https://doi.org/10.1111/1462-2920.14246

Stopnisek, N., Zühlke, D., Carlier, A., et al, Molecular mechanisms underlying the close association between soil Burkholderia and fungi. ISME Journal 10: 1, 253–264. https://doi.org/10.1038/ismej.2015.73 

Stopnisek, N., Bodenhausen, N., Frey, B. et al. Preference of Burkholderia sp. for acid soils. Environmental Microbiology 16: 1503-1512. https://doi.org/10.1111/1462-2920.12211  

Kost, T., Stopnisek, N., Agnoli, K. et al. Oxalotrophy, a widespread trait of plant-associated Burkholderia species, is involved in successful root colonization of lupin and maize by Burkholderia phytofirmans. Frontiers in Microbiology 4:421. https://doi.org/10.3389/fmicb.2013.00421  

Stopnišek, N., Gubry-Rangin, C., Höfferle, Š. et al. Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment. Applied and Environmental Microbiology 76:22, 7626–7634.https://doi.org/10.1128/AEM.00595-10