Voglauer, E. M., Alteio, L. V., Pracser, N., Thalguter, S., Quijada, N. M., Wagner, M., & Rychli, K. (2025). Listeria monocytogenes colonises established multispecies biofilms and resides within them without altering biofilm composition or gene expression. Microbiological Research, 292, 127997. https://doi.org/10.1016/j.micres.2024.127997

Samarra, A., Alcañiz, A. J., Martínez-Costa, C., Marina, A., Comas, I., Segata, N., Quijada, N. M., & Collado, M. C. (2025). Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-61154-w

Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., Breselge, S., Cabrera-Rubio, R., Calvete-Torre, I., Coakley, M., Cobo-Díaz, J. F., De Filippis, F., Dey, H., Leech, J., Klaassens, E. S., … Pasolli, E. (2024). Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Cell, 187(20), 5775-5795.e15. https://doi.org/10.1016/j.cell.2024.07.039

Rodriguez, J., Cordaillat-Simmons, M., Badalato, N., Berger, B., Breton, H., de Lahondès, R., Deschasaux-Tanguy, M., Desvignes, C., D’Humières, C., Kampshoff, S., Lavelle, A., Metwaly, A., Quijada, N. M., Seegers, J. F. M. L., Udocor, A., Zwart, H., Fasano, A., Carraturo, F., … Druart, C. (2024). Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges. Microbiome, 12(1). https://doi.org/10.1186/s40168-024-01991-x

Roch, F.-F., Dzieciol, M., Quijada, N. M., Alteio, L. V., Mester, P.-J., & Selberherr, E. (2024). Microbial community structure of plant-based meat alternatives. Npj Science of Food, 8(1). https://doi.org/10.1038/s41538-024-00269-8

Barcenilla, C., Cobo-Díaz, J. F., De Filippis, F., Valentino, V., Cabrera Rubio, R., O’Neil, D., Mahler de Sanchez, L., Armanini, F., Carlino, N., Blanco-Míguez, A., Pinto, F., Calvete-Torre, I., Sabater, C., Delgado, S., Ruas-Madiedo, P., Quijada, N. M., Dzieciol, M., Skírnisdóttir, S., Knobloch, S., … Alvarez-Ordóñez, A. (2024). Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments. Nature Protocols, 19(5), 1291–1310. https://doi.org/10.1038/s41596-023-00949-x

Olmo, R., Quijada, N. M., Morán-Diez, M. E., Hermosa, R., & Monte, E. (2024). Identification of Tomato microRNAs in Late Response to Trichoderma atroviride. International Journal of Molecular Sciences, 25(3), 1617. https://doi.org/10.3390/ijms25031617

Bédard, C., Pageau, A., Fijarczyk, A., Mendoza-Salido, D., Alcañiz, A. J., Després, P. C., Durand, R., Plante, S., Alexander, E. M. M., Rouleau, F. D., Jordan, D. F., Jay, A., Giguère, M., Bernier, M., Sharma, J., Maroc, L., Gervais, N. C., Menon, A. C. T., Gagnon-Arsenault, I., … Landry, C. R. (2024). FungAMR: A comprehensive portrait of antimicrobial resistance mutations in fungi. https://doi.org/10.1101/2024.10.07.617009

De Filippis, F., Valentino, V., Yap, M., Cabrera-Rubio, R., Barcenilla, C., Carlino, N., Cobo-Díaz, J. F., Quijada, N. M., Calvete-Torre, I., Ruas-Madiedo, P., Sabater, C., Sequino, G., Pasolli, E., Wagner, M., Margolles, A., Segata, N., Álvarez-Ordóñez, A., Cotter, P. D., & Ercolini, D. (2024). Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities. Npj Biofilms and Microbiomes, 10(1). https://doi.org/10.1038/s41522-024-00541-5

Vötterl, J. C., Lerch, F., Schwartz-Zimmermann, H. E., Sassu, E. L., Schwarz, L., Renzhammer, R., Bünger, M., Koger, S., Sharma, S., Sener-Aydemir, A., Quijada, N. M., Selberherr, E., Berthiller, F., & Metzler-Zebeli, B. U. (2023). Plant-oriented microbiome inoculum modulates age-related maturation of gut-mucosal expression of innate immune and barrier function genes in suckling and weaned piglets. Journal of Animal Science, 101. https://doi.org/10.1093/jas/skad165

Lourenco, A., Li, F., Quijada, N. M., Duffy, G., Tobin, J. T., Butler, F., Jordan, K., & O’Brien, T. (2023). Draft Genome Sequences of Bacillus licheniformis and Bacillus paralicheniformis Strains Isolated from Irish Skim Milk Powder. Microbiology Resource Announcements, 12(7). https://doi.org/10.1128/mra.00137-23

Pohlin, F., Frei, C., Meyer, L. C. R., Roch, F.-F., Quijada, N. M., Conrady, B., Neubauer, V., Hofmeyr, M., Cooper, D., Stalder, G., & Wetzels, S. U. (2023). Capture and transport of white rhinoceroses (Ceratotherium simum) cause shifts in their fecal microbiota composition towards dysbiosis. Conservation Physiology, 11(1). https://doi.org/10.1093/conphys/coad089

Quijada, N. M., Dzieciol, M., Schmitz-Esser, S., Wagner, M., & Selberherr, E. (2022). Metatranscriptomic Analyses Unravel Dynamic Changes in the Microbial and Metabolic Transcriptional Profiles in Artisanal Austrian Hard-Cheeses During Ripening. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.813480

Lerch, F., Vötterl, J. C., Schwartz-Zimmermann, H. E., Sassu, E. L., Schwarz, L., Renzhammer, R., Bünger, M., Sharma, S., Koger, S., Sener-Aydemir, A., Quijada, N. M., Selberherr, E., Kummer, S., Berthiller, F., & U. Metzler-Zebeli, B. (2022). Exposure to plant-oriented microbiome altered jejunal and colonic innate immune response and barrier function more strongly in suckling than in weaned piglets. Journal of Animal Science, 100(11). https://doi.org/10.1093/jas/skac310

Quijada, N. M., Abreu, I., Reguera, M., Bonilla, I., & Bolaños, L. (2022). Boron nutrition affects growth, adaptation to stressful environments, and exopolysaccharide synthesis of Ensifer meliloti. Rhizosphere, 22, 100534. https://doi.org/10.1016/j.rhisph.2022.100534

Olmo, R., Wetzels, S. U., Armanhi, J. S. L., Arruda, P., Berg, G., Cernava, T., Cotter, P. D., Araujo, S. C., de Souza, R. S. C., Ferrocino, I., Frisvad, J. C., Georgalaki, M., Hansen, H. H., Kazou, M., Kiran, G. S., Kostic, T., Krauss-Etschmann, S., Kriaa, A., Lange, L., … Wagner, M. (2022). Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.834622

Sharon, I., Quijada, N. M., Pasolli, E., Fabbrini, M., Vitali, F., Agamennone, V., Dötsch, A., Selberherr, E., Grau, J. H., Meixner, M., Liere, K., Ercolini, D., de Filippo, C., Caderni, G., Brigidi, P., & Turroni, S. (2022). The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients, 14(14), 2872. https://doi.org/10.3390/nu14142872

Zwirzitz, B., Wetzels, S. U., Dixon, E. D., Fleischmann, S., Selberherr, E., Thalguter, S., Quijada, N. M., Dzieciol, M., Wagner, M., & Stessl, B. (2021). Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.632935

Wagner, E., Zaiser, A., Leitner, R., Quijada, N. M., Pracser, N., Pietzka, A., Ruppitsch, W., Schmitz-Esser, S., Wagner, M., & Rychli, K. (2020). Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains. BMC Genomics, 21(1). https://doi.org/10.1186/s12864-020-07263-w

Quijada, N. M., Hernández, M., & Rodríguez-Lázaro, D. (2020). High-throughput sequencing and food microbiology. Advances in Food and Nutrition Research, 275–300. https://doi.org/10.1016/bs.afnr.2019.10.003

Abdelhamid, M. K., Quijada, N. M., Dzieciol, M., Hatfaludi, T., Bilic, I., Selberherr, E., Liebhart, D., Hess, C., Hess, M., & Paudel, S. (2020). Co-infection of Chicken Layers With Histomonas meleagridis and Avian Pathogenic Escherichia coli Is Associated With Dysbiosis, Cecal Colonization and Translocation of the Bacteria From the Gut Lumen. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.586437

Hernández, M., Quijada, N. M., Rodríguez-Lázaro, D., & Eiros, J. M. (2020). Aplicación de la secuenciación masiva y la bioinformática al diagnóstico microbiológico clínico. Revista Argentina de Microbiología, 52(2), 150–161. https://doi.org/10.1016/j.ram.2019.06.003

Quijada, N. M., Bodas, R., Lorenzo, J. M., Schmitz-Esser, S., Rodríguez-Lázaro, D., & Hernández, M. (2020). Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs. Biomolecules, 10(8), 1179. https://doi.org/10.3390/biom10081179

Quijada, N. M., Schmitz-Esser, S., Zwirzitz, B., Guse, C., Strachan, C. R., Wagner, M., Wetzels, S. U., Selberherr, E., & Dzieciol, M. (2020). Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi. Foods, 9(12), 1851. https://doi.org/10.3390/foods9121851

Quijada, N. M., Hernández, M., Oniciuc, E.-A., Eiros, J. M., Fernández-Natal, I., Wagner, M., & Rodríguez-Lázaro, D. (2019). Oxacillin-susceptible mecA-positive Staphylococcus aureus associated with processed food in Europe. Food Microbiology, 82, 107–110. https://doi.org/10.1016/j.fm.2019.01.021

Klein-Jöbstl, D., Quijada, N. M., Dzieciol, M., Feldbacher, B., Wagner, M., Drillich, M., Schmitz-Esser, S., & Mann, E. (2019). Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves’ gastrointestinal microbiota. PLOS ONE, 14(8), e0220554. https://doi.org/10.1371/journal.pone.0220554

Hernández, M., de Frutos, M., Rodríguez-Lázaro, D., López-Urrutia, L., Quijada, N. M., & Eiros, J. M. (2019). Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.03331

Quijada, N. M., Rodríguez-Lázaro, D., Eiros, J. M., & Hernández, M. (2019). TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics, 35(21), 4207–4212. https://doi.org/10.1093/bioinformatics/btz220

Hernández, M., Quijada, N. M., Lorente, L. L.-U., de Frutos, M., Rodríguez-Lázaro, D., & Eiros, J. M. (2018). Infrequent isolation of extensively drug-resistant (XDR) Klebsiella pneumoniae resistant to colistin in Spain. International Journal of Antimicrobial Agents, 51(3), 531–533. https://doi.org/10.1016/j.ijantimicag.2017.12.033

Quijada, N. M., De Filippis, F., Sanz, J. J., García-Fernández, M. del C., Rodríguez-Lázaro, D., Ercolini, D., & Hernández, M. (2018). Different Lactobacillus populations dominate in “Chorizo de León” manufacturing performed in different production plants. Food Microbiology, 70, 94–102. https://doi.org/10.1016/j.fm.2017.09.009

Quijada, N. M., Mann, E., Wagner, M., Rodríguez-Lázaro, D., Hernández, M., & Schmitz-Esser, S. (2018). Autochthonous facility-specific microbiota dominates washed-rind Austrian hard cheese surfaces and its production environment. International Journal of Food Microbiology, 267, 54–61. https://doi.org/10.1016/j.ijfoodmicro.2017.12.025

Adserias-Garriga, J., Hernández, M., Quijada, N. M., Rodríguez Lázaro, D., Steadman, D., & Garcia-Gil, J. (2017). Daily thanatomicrobiome changes in soil as an approach of postmortem interval estimation: An ecological perspective. Forensic Science International, 278, 388–395. https://doi.org/10.1016/j.forsciint.2017.07.017

Hernández, M., Iglesias, M. R., Rodríguez-Lázaro, D., Gallardo, A., Quijada, N., Miguela-Villoldo, P., Campos, M. J., Píriz, S., López-Orozco, G., de Frutos, C., Sáez, J. L., Ugarte-Ruiz, M., Domínguez, L., & Quesada, A. (2017). Co-occurrence of colistin-resistance genes mcr-1 and mcr-3 among multidrug-resistant Escherichia coli isolated from cattle, Spain, September 2015. Eurosurveillance, 22(31). https://doi.org/10.2807/1560-7917.es.2017.22.31.30586

Sánchez-Benito, R., Iglesias, M. R., Quijada, N. M., Campos, M. J., Ugarte-Ruiz, M., Hernández, M., Pazos, C., Rodríguez-Lázaro, D., Garduño, E., Domínguez, L., & Quesada, A. (2017). Escherichia coli ST167 carrying plasmid mobilisable mcr-1 and blaCTX-M-15 resistance determinants isolated from a human respiratory infection. International Journal of Antimicrobial Agents, 50(2), 285–286. https://doi.org/10.1016/j.ijantimicag.2017.05.005

Adserias‐Garriga, J., Quijada, N. M., Hernandez, M., Rodríguez Lázaro, D., Steadman, D., & Garcia‐Gil, L. J. (2017). Dynamics of the oral microbiota as a tool to estimate time since death. Molecular Oral Microbiology, 32(6), 511–516. Portico. https://doi.org/10.1111/omi.12191

Quijada, N. M., Fongaro, G., Barardi, C. R. M., Hernández, M., & Rodríguez-Lázaro, D. (2016). Propidium Monoazide Integrated with qPCR Enables the Detection and Enumeration of Infectious Enteric RNA and DNA Viruses in Clam and Fermented Sausages. Frontiers in Microbiology, 7. https://doi.org/10.3389/fmicb.2016.02008

Rubio, M. B., Quijada, N. M., Pérez, E., Domínguez, S., Monte, E., & Hermosa, R. (2014). Identifying Beneficial Qualities of Trichoderma parareesei for Plants. Applied and Environmental Microbiology, 80(6), 1864–1873. https://doi.org/10.1128/aem.03375-13