Aslam, U., Scott, W. T., Mariën, Q., Sabbe, K., De Wever, H., & Ganigué, R. (2026). Experimental and model-based analysis of H₂/CO₂ mixotrophic lactate metabolism reveals thermodynamic constraints on carbon efficiency in Clostridium luticellarii. Chemical Engineering Journal, 179806. https://doi.org/10.1016/j.cej.2026.179806

Scott, W. T., Nataya, E. D., Belzer, C., & Schaap, P. J. (2026). Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape. ISME Communications, 6(1), ycag077. https://doi.org/10.1093/ismeco/ycag077

Georgakilas, G. K., Metcalfe, B., Bize, A., Crowther, M., Fernandez, E., Alonso Villela, S. M., Owen, S., Wittner, R., Corrales, D. C., von Gladiss, A., Blomberg, P., Andrabi, M., Aceves Lara, C. A., Mattila, H., Wiebe, M., Dalamagas, T., Koehorst, J. J., & others. (2026). MIFE and MIFD: Minimum information for fermentation experiments and devices. GigaScience. https://doi.org/10.1093/gigascience/giag038

Lesiczka, P. M., Azagi, T., Krawczyk, A. I., Scott, W. T., Dirks, R. P., Simo, L., Dobler, G., Nijsse, B., Schaap, P. J., Sprong, H., & Koehorst, J. J. (2025). Deep sequencing of 16 Ixodes ricinus ticks unveils insights into their interactions with endosymbionts. mSystems. https://doi.org/10.1128/msystems.00507-25

Scott, W. T., Rockx, S., Mariën, Q., Regueira, A., Candry, P., Ganigué, R., Koehorst, J. J., & Schaap, P. J. (2025). Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations. Computational and Structural Biotechnology Journal. https://doi.org/10.1016/j.csbj.2025.01.013

Ioannou, A., Berkhout, M. D., Scott, W. T., Blijenberg, B., Boeren, S., Mank, M., Knol, J., & Belzer, C. (2024). Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides. The ISME Journal, 18(1). https://doi.org/10.1093/ismejo/wrae209

Zhang, C., Sánchez, B. J., Li, F., Eiden, C. W. Q., Scott, W. T., Liebal, U. W., Blank, L. M., Mengers, H. G., Anton, M., Rangel, A. T., Mendoza, S. N., Zhang, L., Nielsen, J., Lu, H., & Kerkhoven, E. J. (2024). Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community. Molecular Systems Biology, 20(10), 1134–1150. https://doi.org/10.1038/s44320-024-00060-7

Atasoy, M., Scott, W., Jr, Van Gijn, K., Koehorst, J., Smidt, H., & Langenhoff, A. (2023b). Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent. Bioresource Technology, 372, 128659. https://doi.org/10.1016/j.biortech.2023.128659

Atasoy, M., Scott, W., Jr, Van Gijn, K., Koehorst, J., Smidt, H., & Langenhoff, A. (2023). Microbial dynamics and bioreactor performance are interlinked with organic matter removal from wastewater treatment plant effluent. Bioresource Technology, 372, 128659. https://doi.org/10.1016/j.biortech.2023.128659

Angthong, P., Uengwetwanit, T., Uawisetwathana, U., Koehorst, J. J., Arayamethakorn, S., Schaap, P. J., Santos, V. M. D., Phromson, M., Karoonuthaisiri, N., Chaiyapechara, S., & Rungrassamee, W. (2023). Investigating host-gut microbial relationship in Penaeus monodon upon exposure to Vibrio harveyi. Aquaculture, 567, 739252. https://doi.org/10.1016/j.aquaculture.2023.739252

Jiménez-Volkerink, S. N., Jordán, M., Smidt, H., Minguillón, C., Vila, J., & Grifoll, M. (2023). Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil. The Science of the Total Environment, 907, 167832. https://doi.org/10.1016/j.scitotenv.2023.167832

Scott, W. T., Henriques, D., Smid, E. J., Notebaart, R. A., & Balsa‐Canto, E. (2023). Dynamic genome‐scale modeling of Saccharomyces cerevisiae unravels mechanisms for ester formation during alcoholic fermentation. Biotechnology and Bioengineering, 120(7), 1998–2012. https://doi.org/10.1002/bit.28421

Atasoy, M., Ordóñez, A. Á., Cenian, A., Djukić-Vuković, A., Lund, P. A., Ozogul, F., Trček, J., Ziv, C., & De Biase, D. (2023). Exploitation of microbial activities at low pH to enhance planetary health. FEMS Microbiology Reviews, 48(1). https://doi.org/10.1093/femsre/fuad062

Wu, K., Atasoy, M., Zweers, H., Rijnaarts, H., Langenhoff, A., & Fernandes, T. V. (2023). Impact of wastewater characteristics on the removal of organic micropollutants by Chlorella sorokiniana. Journal of Hazardous Materials, 453, 131451. https://doi.org/10.1016/j.jhazmat.2023.131451

Atasoy, M. (2023). Advances in environmental bioprocess technology for an effective transition to a green circular economy. In G. Mannina, A. Pandey, & R. Sirohi (Eds.), Current developments in biotechnology and bioengineering (pp. 291–314). Elsevier. https://doi.org/10.1016/B978-0-323-99920-5.00016-0

Scott, W. T., Benito-Vaquerizo, S., Zimmermann, J., Bajić, D., Heinken, A., Suarez-Diez, M., & Schaap, P. J. (2023). A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia. PLoS Computational Biology, 19(8), e1011363. https://doi.org/10.1371/journal.pcbi.1011363

Zhang, C., Atashgahi, S., Bosma, T. N. P., Peng, P., & Smidt, H. (2022). Organohalide respiration potential in marine sediments from Aarhus Bay. FEMS Microbiology Ecology, 98(8). https://doi.org/10.1093/femsec/fiac073

Cetecioglu, Z., Atasoy, M., Cenian, A., Sołowski, G., Trček, J., Ugurlu, A., & Sedlakova-Kadukova, J. (2022). Bio-Based Processes for Material and Energy Production from Waste Streams under Acidic Conditions. Fermentation, 8(3), 115. https://doi.org/10.3390/fermentation8030115

Pinto, G., Shetty, S. A., Zoetendal, E. G., Gonçalves, R. F. S., Pinheiro, A. C., Almeida, C., Azeredo, J., & Smidt, H. (2022). An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota. Npj Biofilms and Microbiomes, 8(1). https://doi.org/10.1038/s41522-022-00334-8

Jiménez-Volkerink, S. N., Vila, J., Jordán, M., Minguillón, C., Smidt, H., & Grifoll, M. (2022). Multi-Omic Profiling of a Newly Isolated Oxy-PAH Degrading Specialist from PAH-Contaminated Soil Reveals Bacterial Mechanisms to Mitigate the Risk Posed by Polar Transformation Products. Environmental Science & Technology, 57(1), 139–149. https://doi.org/10.1021/acs.est.2c05485

Benito-Vaquerizo, S., Nouse, N., Schaap, P. J., Hugenholtz, J., Brul, S., López-Contreras, A. M., Santos, V. a. P. M. D., & Suarez-Diez, M. (2022). Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii. Frontiers in Microbiology, 13. https://doi.org/10.3389/fmicb.2022.1064013

Poncheewin, W., Van Diepeningen, A. D., Van Der Lee, T. a. J., Suarez-Diez, M., & Schaap, P. J. (2022). Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-14913-4

Nijsse, B., Schaap, P. J., & Koehorst, J. J. (2022). FAIR data station for lightweight metadata management and validation of omics studies. GigaScience, 12. https://doi.org/10.1093/gigascience/giad014

Atasoy, M., & Cetecioglu, Z. (2022). The effects of pH on the production of volatile fatty acids and microbial dynamics in long-term reactor operation. Journal of Environmental Management, 319, 115700. https://doi.org/10.1016/j.jenvman.2022.115700

Shetty, S. A., Kostopoulos, I., Geerlings, S. Y., Smidt, H., De Vos, W. M., & Belzer, C. (2022). Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. The ISME Journal, 16(9), 2144–2159. https://doi.org/10.1038/s41396-022-01255-2

Azagi, T., Dirks, R. P., Yebra-Pimentel, E. S., Schaap, P. J., Koehorst, J. J., Esser, H. J., & Sprong, H. (2022). Assembly and Comparison of Ca. Neoehrlichia mikurensis Genomes. Microorganisms, 10(6), 1134. https://doi.org/10.3390/microorganisms10061134

Shetty, S. A., Kuipers, B., Atashgahi, S., Aalvink, S., Smidt, H., & De Vos, W. M. (2022). Inter-species metabolic interactions in an in-vitro minimal human gut microbiome of core bacteria. Npj Biofilms and Microbiomes, 8(1). https://doi.org/10.1038/s41522-022-00275-2

Waagmeester, A., Willighagen, E. L., Su, A. I., Kutmon, M., Gayo, J. E. L., Fernández-Álvarez, D., Groom, Q., Schaap, P. J., Verhagen, L. M., & Koehorst, J. J. (2021). A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. BMC Biology, 19(1). https://doi.org/10.1186/s12915-020-00940-y

Kleerebezem, R., Stouten, G., Koehorst, J., Langenhoff, A., Schaap, P., & Smidt, H. (2021). Experimental infrastructure requirements for quantitative research on microbial communities. Current Opinion in Biotechnology, 67, 158–165. https://doi.org/10.1016/j.copbio.2021.01.017

Morales, D., Shetty, S. A., López-Plaza, B., Gómez-Candela, C., Smidt, H., Marín, F. R., & Soler-Rivas, C. (2021). Modulation of human intestinal microbiota in a clinical trial by consumption of a β-d-glucan-enriched extract obtained from Lentinula edodes. European Journal of Nutrition, 60(6), 3249–3265. https://doi.org/10.1007/s00394-021-02504-4

Shetty, S. A., Boeren, S., Bui, T. P. N., Smidt, H., & De Vos, W. M. (2020). Unravelling lactate‐acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. Environmental Microbiology, 22(11), 4863–4875. https://doi.org/10.1111/1462-2920.15269

Poncheewin, W., Hermes, G. D. A., Van Dam, J. C. J., Koehorst, J. J., Smidt, H., & Schaap, P. J. (2020). NG-TAX 2.0: A Semantic Framework for High-ThroughPut Amplicon Analysis. Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.01366

Peng, P., Goris, T., Lu, Y., Nijsse, B., Burrichter, A., Schleheck, D., Koehorst, J. J., Liu, J., Sipkema, D., Damste, J. S. S., Stams, A. J. M., Häggblom, M. M., Smidt, H., & Atashgahi, S. (2020). Organohalide-respiring Desulfoluna species isolated from marine environments. The ISME Journal, 14(3), 815–827. https://doi.org/10.1038/s41396-019-0573-y

Peng, P., Lu, Y., Bosma, T. N., Nijenhuis, I., Nijsse, B., Shetty, S. A., Ruecker, A., Umanets, A., Ramiro-Garcia, J., Kappler, A., Sipkema, D., Smidt, H., & Atashgahi, S. (2020). Metagenomic- and Cultivation-Based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes. Microorganisms, 8(5), 665. https://doi.org/10.3390/microorganisms8050665