Publications

Bustamante, M., Mei, S., Daras, I. M., van Doorn, G. S., Falcao Salles, J., & de Vos, M. G. J. (2025). An eco-evolutionary perspective on antimicrobial resistance in the context of One Health. iScience , 28(1), Article 111534. https://doi.org/10.1016/j.isci.2024.111534

Li, J., Li, Y., Zhang, N., Shen, Z., Shen, B., Li, R., Deng, X., Shen, Q., & Salles, J. F. (2025). Risk assessment of antibiotic resistance genes in rhizosphere soil during tomato growth under bio-control bacterial inoculation. Journal of Cleaner Production, 493, Article 144911. https://doi.org/10.1016/j.jclepro.2025.144911

Voulgari-Kokota, A., Boatta, F., Rijkers, R., Wertheim, B., Beukeboom, L. W., Ellers, J., & Salles, J. F. (2025). High-sugar diet leads to loss of beneficial probiotics in housefly larvae guts. The ISME journal, 18(1), Article wrae193. https://doi.org/10.1093/ismejo/wrae193

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2025). Microbial solutions must be deployed against climate catastrophe. Nature Reviews Microbiology, 23(1). https://doi.org/10.1038/s41579-024-01123-0

Voulgari-Kokota, A., Falcao Salles, J., & Schoemaker, R. G. (2024). Aggression shapes the gut microbiome: A study in rats. PLoS ONE, 19(10), Article e0312423. https://doi.org/10.1371/journal.pone.0312423

Liu, X., & Salles, J. F. (2024). Bridging ecological assembly process and community stability upon bacterial invasions. The ISME journal, 18(1), Article wrae066. https://doi.org/10.1093/ismejo/wrae066

Mei, S., Wang, M., Salles, J. F., & Hackl, T. (2024). Diverse rhizosphere-associated Pseudomonas genomes from along a Wadden Island salt marsh transition zone. Scientific Data, 11(1), Article 1140. https://doi.org/10.1038/s41597-024-03961-2

Liu, X., & Salles, J. F. (2024). Drivers and consequences of microbial community coalescence. The ISME journal, 18(1), Article wrae179. https://doi.org/10.1093/ismejo/wrae179

Javůrková, V. G., Brlík, V., Heneberg, P., Požgayová, M., Procházka, P., Dietz, M. W., Salles, J. F., & Tieleman, B. I. (2024). Host traits rather than migration and molting strategies explain feather bacterial load in Palearctic passerines. Iscience, 27(11), Article 111079. https://doi.org/10.1016/j.isci.2024.111079

Voulgari-Kokota, A., Slijfer, R., Beukeboom, L. W., Falcao Salles, J., & Wertheim, B. (2024). Immunity-related genes can serve as early diagnostic markers for infection in housefly rearing systems. Journal of Insects as Food and Feed, 10(9), 1607-1621. https://doi.org/10.1163/23524588-20230094

Liu, X., & Salles, J. F. (2024). Lose-lose consequences of bacterial community-driven invasions in soil. Microbiome, 12(1), Article 57. https://doi.org/10.1186/s40168-024-01763-7

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. The ISME journal, 18(1). https://doi.org/10.1093/ismejo/wrae219

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Microbiology, 9(12), 3084-3085. https://doi.org/10.1038/s41564-024-01861-0

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Reviews Earth and Environment, 6, 4-5. https://doi.org/10.1038/s43017-024-00611-4

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. FEMS microbiology ecology, 100(11), Article fiae144. https://doi.org/10.1093/femsec/fiae144

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Communications biology, 7(1), Article 1466. https://doi.org/10.1038/s42003-024-07108-2

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Communications, 15(1), 9637. https://doi.org/10.1038/s41467-024-53680-w

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Sustainable Microbiology, 1(1), qvae029. https://doi.org/10.1093/sumbio/qvae029

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Biodiversity, 3(34). https://doi.org/10.1038/s44185-024-00066-2

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. NPJ biofilms and microbiomes, 10(1), Article 122. https://doi.org/10.1038/s41522-024-00591-9

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Msystems, 10(1), Article e0141624. https://doi.org/10.1128/msystems.01416-24

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. Communications Earth & Environment, 5(1), Article 672. https://doi.org/10.1038/s43247-024-01817-6

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Climate Action, 3, Article 102. https://doi.org/10.1038/s44168-024-00179-1

Peixoto, R., Voolstra, C. R., Stein, L. Y., Hugenholtz, P., Salles, J. F., Amin, S. A., Häggblom, M., Gregory, A., Makhalanyane, T. P., Wang, F., Agbodjato, N. A., Wang, Y., Jiao, N., Lennon, J. T., Ventosa, A., Bavoil, P. M., Miller, V., & Gilbert, J. A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Sustainable Agriculture, 2(1), Article 23. https://doi.org/10.1038/s44264-024-00033-1

Álvarez, V. E., El Mujtar, V. A., Falcão Salles, J., Jia, X., Castán, E., Cardozo, A. G., & Tittonell, P. A. (2024). Micro-environmental variation in soil microbial biodiversity in forest frontier ecosystems: Implications for sustainability assessments. Sustainability, 16(3), Article 1236. https://doi.org/10.3390/su16031236

Genesiska, Salles, J. F., & Tiedge, K. J. (2024). Untangling the rhizosphere specialized metabolome. Phytochemistry reviews. https://doi.org/10.1007/s11101-024-10036-y

Bustamante, M., Koopman, F., Martens, J., Brons, J. K., DelaFuente, J., Hackl, T., Kuipers, O. P., van Doorn, G. S., & de Vos, M. G. J. (2024). Community context influences the conjugation efficiency of Escherichia coli. FEMS Microbes, 5, Article xtae023. https://doi.org/10.1093/femsmc/xtae023

Araujo, A. S. F., Jia, X., Miranda, A. R. L., Pereira, A. P. D. A., Melo, V. M. M., Rocha, S. M. B., Costa, R. M., Saraiva, T. C. D. S., Mendes, L. W., & Salles, J. F. (2023). Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil. Chemosphere, 313, Article 137487. https://doi.org/10.1016/j.chemosphere.2022.137487

Liu, X., Mei, S., & Falcao Salles, J. (2023). Inoculated microbial consortia perform better than single strains in living soil: A meta-analysis. Applied Soil Ecology, 190, Article 105011. https://doi.org/10.1016/j.apsoil.2023.105011

Li, Y., Deng, X., Zhang, N., Shen, Z., Li, R., Shen, Q., & Salles, J. F. (2023). Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion. One Health, 16, Article 100481. https://doi.org/10.1016/j.onehlt.2023.100481

Wang, Y., Jiménez, D. J., Zhang, Z., & van Elsas, J. D. (2023). Functioning of a tripartite lignocellulolytic microbial consortium cultivated under two shaking conditions: A metatranscriptomic study. Biotechnology for Biofuels and Bioproducts, 16(1), Article 54. https://doi.org/10.1186/s13068-023-02289-0

Brinker, P., Chen, F., Ben Chehida, Y., Beukeboom, L., Fontaine, M., & Falcao Salles, J. (2023). Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica , but not in the presence of the endosymbiont Wolbachia. Molecular Ecology, 32(23), 6644-6658. https://doi.org/10.1111/mec.16699

Gurung, K., Vink, S. N., Salles, J. F., & Wertheim, B. (2023). More persistent bacterial than fungal associations in the microbiota of a pest insect. Journal of Pest Science, 96, 785–796. https://doi.org/10.1007/s10340-022-01524-1

Deng, X., Zhang, N., Li, Y., Zhu, C., Qu, B., Liu, H., Li, R., Bai, Y., Shen, Q., & Falcao Salles, J. (2022). Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities. New Phytologist, 235(4), 1558-1574. https://doi.org/10.1111/nph.18221

Yu, Y., van der Zwaag, M., Wedman, J. J., Permentier, H., Plomp, N., Jia, X., Kanon, B., Eggens-Meijer, E., Buist, G., Harmsen, H., Kok, J., Salles, J. F., Wertheim, B., Hayflick, S. J., Strauss, E., Grzeschik, N. A., Schepers, H., & Sibon, O. C. M. (2022). Coenzyme A precursors flow from mother to zygote and from microbiome to host. Molecular Cell, 82(14), 2650-2665.e12. https://doi.org/10.1016/j.molcel.2022.05.006

Saatkamp, H. W., Aartsma, Y., Hogeveen, H., Augustijn, M., Baumann, A., Beukeboom, L. W., Borghuis, A., Bovenkerk, B., van der Bruggen, M., Companjen, M. H., Dörper, A., Salles, J. F., van der Fels-Klerx, H. J., Fischer, A. R. H., Haenen, O., Hosseini, A., van den Hurk, J., Jacobs, P., Jansen, W. L., ... Dicke, M. (2022). Development of sustainable business models for insect-fed poultry production: Opportunities and risks. Journal of Insects as Food and Feed, 8(12), 1469-1483. https://doi.org/10.3920/JIFF2021.0216

van der Goot, E., Vink, S. N., van Vliet, D., van Spronsen, F. J., Falcao Salles, J., & van der Zee, E. A. (2022). Gut-microbiome composition in response to phenylketonuria depends on dietary phenylalanine in BTBR Pah^enu2 mice. Frontiers in nutrition, 8, Article 735366. https://doi.org/10.3389/fnut.2021.735366

Dietz, M., Matson, K. D., Versteegh, M., van der Velde, M., Parmentier, H. K., Arts, J. A. J., Falcao Salles, J., & Tieleman, B. I. (2022). Gut microbiota of homing pigeons shows summer–winter variation under constant diet indicating a substantial effect of temperature. Animal microbiome, 4, Article 64. https://doi.org/10.1186/s42523-022-00216-6

Vogel, M., Shah, P. N., Voulgari-Kokota, A., Maistrou, S., Aartsma, Y., Beukeboom, L. W., Salles, J. F., van Loon, J. J. A., Dicke, M., & Wertheim, B. (2022). Health of the black soldier fly and house fly under mass-rearing conditions: Innate immunity and the role of the microbiome. Journal of Insects as Food and Feed, 8(8), 857-878. https://doi.org/10.3920/JIFF2021.0151

Voulgari-Kokota, A., Beukeboom, L. W., Wertheim, B., & Salles, J. F. (2022). Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria. Scientific Reports, 12(1), Article 11132. https://doi.org/10.1038/s41598-022-15186-7

Mawarda, P. C., Mallon, C. A., Le Roux, X., van Elsas, J. D., & Salles, J. F. (2022). Interactions between bacterial inoculants and native soil bacterial community: The case of spore-forming Bacillus spp. FEMS microbiology ecology, 98(12), 1-11. https://doi.org/10.1093/femsec/fiac127

Bisschop, K., Kortenbosch, H. H., van Eldijk, T. J. B., Mallon, C. A., Salles, J. F., Bonte, D., & Etienne, R. S. (2022). Microbiome heritability and its role in adaptation of hosts to novel resources. Frontiers in Microbiology, 13, 703183. Article 703183. https://doi.org/10.3389/fmicb.2022.703183

Frąc, M., Hannula, E. S., Bełka, M., Salles, J. F., & Jedryczka, M. (2022). Soil mycobiome in sustainable agriculture. Frontiers in Microbiology, 13, Article 1033824. https://doi.org/10.3389/fmicb.2022.1033824

Mawarda, P., Lakke, S. L., van Elsas, J. D., & Falcao Salles, J. (2022). Temporal dynamics of the soil bacterial community following Bacillus invasion. iScience , 25(5), Article 104185. https://doi.org/10.1016/j.isci.2022.104185

Mawarda, P. C., Le Roux, X., Uribe Acosta, M., van Elsas, J. D., & Falcao Salles, J. (2022). The impact of protozoa addition on the survivability of Bacillus inoculants and soil microbiome dynamics. ISME Communications, 2, Article 82 (2022). https://doi.org/10.1038/s43705-022-00166-9

Liu, X., Le Roux, X., & Salles, J. F. (2022). The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges. Iscience, 25(3), Article 103821. https://doi.org/10.1016/j.isci.2022.103821

van Veelen, H. P. J., Salles, J. F., Matson, K. D., van Doorn, G. S., van der Velde, M., & Tieleman, B. I. (2022). The microbial environment modulates non-genetic maternal effects on egg immunity. Animal microbiome, 4(1), Article 44. https://doi.org/10.1186/s42523-022-00195-8

Jia, X., Dini-Andreote, F., & Salles, J. F. (2022). Unravelling the interplay of ecological processes structuring the bacterial rare biosphere. ISME Communications, 2(1), Article 96. https://doi.org/10.1038/s43705-022-00177-6

Chen, Q., Deng, X., Elzenga, J. T. M., & van Elsas, J. D. (2022). Effect of soil bacteriomes on mycorrhizal colonization by Rhizophagus irregularis: Interactive effects on maize (Zea mays L.) growth under salt stress. Biology and Fertility of Soils , 58, 515-525. https://doi.org/10.1007/s00374-022-01636-x

Angulo, V., Beriot, N., Garcia-Hernandez, E., Li, E., Masteling, R., & Lau, J. A. (2022). Plant-microbe eco-evolutionary dynamics in a changing world. New Phytologist, 234(6), 1919-1928. https://doi.org/10.1111/nph.18015

Oberman, K., Hovens, I., de Haan, J., Falcao-Salles, J., van Leeuwen, B., & Schoemaker, R. (2021). Acute pre-operative ibuprofen improves cognition in a rat model for postoperative cognitive dysfunction. Journal of neuroinflammation, 18(1), 1-13. Article 156. https://doi.org/10.1186/s12974-021-02206-y

Vink, S. N., Chrysargyris, A., Tzortzakis, N., & Salles, J. F. (2021). Bacterial community dynamics varies with soil management and irrigation practices in grapevines (Vitis vinifera L.). Applied Soil Ecology, 158, Article 103807. https://doi.org/10.1016/j.apsoil.2020.103807

Hovens, I. B., van Leeuwen, B. L., Falcao-Salles, J., de Haan, J. J., & Schoemaker, R. G. (2021). Enteral enriched nutrition to prevent cognitive dysfunction after surgery: A study in rats. Brain, behavior, & immunity - health, 16, Article 100305. https://doi.org/10.1016/j.bbih.2021.100305

Vink, S. N., Dini-Andreote, F., Höfle, R., Kicherer, A., & Salles, J. F. (2021). Interactive effects of scion and rootstock genotypes on the root microbiome of grapevines (Vitis spp. L.). Applied Sciences, 11(4), Article 1615. https://doi.org/10.3390/app11041615

García Hernández, E., Berg, M. P., Van Oosten, A. R., Smit, C., & Falcão Salles, J. (2021). Linking bacterial communities associated with the environment and the ecosystem engineer Orchestia gammarellus at contrasting salt marsh elevations. Microbial ecology, 82, 537-548. https://doi.org/10.1007/s00248-020-01656-w

Hendriks, K. P., Bisschop, K., Kavanagh, J. C., Kortenbosch, H. H., Larue, A. E. A., Bonte, D., Duijm, E. J., Salles, J. F., Richter Mendoza, F. J., Schilthuizen, M., & Etienne, R. S. (2021). Plant diets of land snail community members are similar in composition but differ in richness. Journal of Molluscan Studies, 87(4), Article eyab041. https://doi.org/10.1093/mollus/eyab041

Deng, X., Zhang, N., Shen, Z., Zhu, C., Liu, H., Xu, Z., Li, R., Shen, Q., & Salles, J. F. (2021). Soil microbiome manipulation triggers direct and possible indirect suppression against Ralstonia solanacearum and Fusarium oxysporum. NPJ biofilms and microbiomes, 7(1), Article 33. https://doi.org/10.1038/s41522-021-00204-9

Wang, Y., Brons, J. K., & van Elsas, J. D. (2021). Considerations on the identity and diversity of organisms affiliated with Sphingobacterium multivorum: Proposal for a new species, Sphingobacterium paramultivorum. Microorganisms, 9(10), Article 2057. https://doi.org/10.3390/microorganisms9102057

Zandbergen, L., Brons, J., Halverson, T., Wolfe, A. J., & de Vos, M. (2021). The good and the bad: Ecological interaction measurements between the urinary microbiota and uropathogens. Frontiers in Microbiology, 12, Article 659450. https://doi.org/10.3389/fmicb.2021.659450

van Vliet, D., van der Goot, E., van Ginkel, W. G., van Faassen, H. J. R., de Blaauw, P., Kema, I. P., Heiner-Fokkema, M. R., van der Zee, E. A., & van Spronsen, F. J. (2022). The increasing importance of LNAA supplementation in phenylketonuria at higher plasma phenylalanine concentrations. Molecular Genetics and Metabolism, 135(1), 27-34. https://doi.org/10.1016/j.ymgme.2021.11.003

Dijkstra, A. M., van Vliet, N., van Vliet, D., Romani, C., Huijbregts, S. C. J., van der Goot, E., Hovens, I. B., van der Zee, E. A., Kema, I. P., Heiner-Fokkema, M. R., & van Spronsen, F. J. (2021). Correlations of blood and brain biochemistry in phenylketonuria: Results from the Pah-enu2 PKU mouse. Molecular Genetics and Metabolism, 134(3), 250-256. https://doi.org/10.1016/j.ymgme.2021.09.004

Wang, Y., Elzenga, T., & van Elsas, J. D. (2021). Effect of culture conditions on the performance of lignocellulose-degrading synthetic microbial consortia. Applied Microbiology and Biotechnology, 105, 7981–7995. https://doi.org/10.1007/s00253-021-11591-6

Hendriks, K. P., Bisschop, K., Kortenbosch, H. H., Kavanagh, J. C., Larue, A. E. A., Phung, C.-C., Bonte, D., Duijm, E. J., Falcão Salles, J., Pigot, A. L., Richter Mendoza, F. J., Schilthuizen, M., Anderson, M. J., Speksnijder, A. G. C. L., & Etienne, R. S. (2021). Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails. Ecology, 102(2), Article e03237. https://doi.org/10.1002/ecy.3237

Ferreira, D. A., da Silva, T. F., Pylro, V. S., Salles, J. F., Andreote, F. D., & Dini-Andreote, F. (2021). Soil microbial diversity affects the plant-root colonization by arbuscular mycorrhizal fungi. Microbial ecology, 82, 100–103. https://doi.org/10.1007/s00248-020-01502-z

Xing, J., Jia, X., Wang, H., Ma, B., Salles, J. F., & Xu, J. (2021). The legacy of bacterial invasions on soil native communities. Environmental Microbiology, 23(2), 669-681. https://doi.org/10.1111/1462-2920.15086

Jurburg, S. D., Assemien, F. L., Beaumelle, L., Salles, J. F., van Elsas, J. D., & Le Roux, X. (2020). A history of extreme disturbance affects the relationship between the abundances of nitrifiers in soil. Biology and Fertility of Soils , 56(8), 1177-1187. https://doi.org/10.1007/s00374-020-01491-8

van der Goot, E., van Spronsen, F. J., Falcão Salles, J., & van der Zee, E. A. (2020). A microbial community ecology perspective on the gut-microbiome-brain axis. Frontiers in endocrinology, 11, 611. Article 611. https://doi.org/10.3389/fendo.2020.00611

Cortes-Tolalpa, L., Wang, Y., Salles, J. F., & van Elsas, J. D. (2020). Comparative genome analysis of the lignocellulose degrading bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15. Frontiers in Microbiology, 11, 248. Article 248. https://doi.org/10.3389/fmicb.2020.00248

Jia, X., Dini-Andreote, F., & Falcão Salles, J. (2020). Comparing the influence of assembly processes governing bacterial community succession based on DNA and RNA data. Microorganisms, 8(6), Article 798. https://doi.org/10.3390/microorganisms8060798

Mawarda, P. C., Le Roux, X., van Elsas, J. D., & Salles, J. F. (2020). Deliberate introduction of invisible invaders: A critical appraisal of the impact of microbial inoculants on soil microbial communities. Soil Biology and Biochemistry, 148, Article 107874. https://doi.org/10.1016/j.soilbio.2020.107874

Engel, F. G., Dini-Andreote, F., Eriksson, B. K., Salles, J. F., de Lima Brossi, M. J., & Matthiessen, B. (2020). Dispersal mitigates bacterial dominance over microalgal competitor in metacommunities. Oecologia, 193(3), 677-687. https://doi.org/10.1007/s00442-020-04707-8

Dicke, M., Eilenberg, J., Salles, J. F., Jensen, A. B., Lecocq, A., Pijlman, G. P., van Loon, J. J. A., & van Oers, M. M. (2020). Edible insects unlikely to contribute to transmission of coronavirus SARS-CoV-2. Journal of Insects as Food and Feed, 6(4), 333-339. https://doi.org/10.3920/JIFF2020.0039

van Veelen, H. P. J., Falcão Salles, J., Matson, K. D., van der Velde, M., & Tieleman, B. I. (2020). Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata. Animal microbiome, 2(1), Article 21. https://doi.org/10.1186/s42523-020-00039-3

Deng, X., Zhang, N., Shen, Z., Zhu, C., Li, R., Salles, J. F., & Shen, Q. (2020). Rhizosphere bacteria assembly derived from fumigation and organic amendment triggers the direct and indirect suppression of tomato bacterial wilt disease. Applied Soil Ecology, 147, Article 103364. https://doi.org/10.1016/j.apsoil.2019.103364

Hernández, E. G., Baraza, E., Smit, C., Berg, M. P., & Falcão Salles, J. (2020). Salt marsh elevation drives root microbial composition of the native invasive grass Elytrigia atherica. Microorganisms, 8(10), 1-19. Article 1619. https://doi.org/10.3390/microorganisms8101619

Pratama, A. A., Terpstra, J., de Oliveria, A. L. M., & Salles, J. F. (2020). The role of rhizosphere bacteriophages in plant health. Trends in Microbiology, 28(9), 709-718. https://doi.org/10.1016/j.tim.2020.04.005

Sternhagen, E. C., Black, K. L., Hartmann , E. DL., Shivega, W. G., Johnson, P. G., McGlynn, R. D., Schmaltz, L. C., Asheim Keller, R. J., Vink, S. N., & Aldrich-Wolfe, L. (2020). Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally managed fields. Applied and environmental microbiology, 86(11), Article 5220. https://doi.org/10.1128/AEM.00052-20

Brons, J., Vink, S. N., de Vos, M., Reuter, S., Dobrindt, U., & van Elsas, J. D. (2020). Fast identification of Escherichia coli in urinary tract infections using a virulence gene based PCR approach in a novel thermal cycler. Journal of microbiological methods, 169, Article 105799. https://doi.org/10.1016/j.mimet.2019.105799

Vink, S. N., Bienkowski, D., Roberts, D. M., Daniell, T. J., & Neilson, R. (2020). Impact of land use and management practices on soil nematode communities of Machair, a low-input calcareous ecosystem of conservation importance. Science of the Total Environment, 738, Article 140164. https://doi.org/10.1016/j.scitotenv.2020.140164

Aldrich-Wolfe, L., Black, K. L., Hartmann, E. D. L., Shivega, W. G., Schmaltz, L. C., McGlynn, R. D., Johnson, P. G., Asheim Keller, R. J., & Vink, S. N. (2020). Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. Mycorrhiza, 30(4), 513-527. https://doi.org/10.1007/s00572-020-00967-7

Tragust, S., Brinker, P., Rossel, N., & Otti, O. (2020). Balancing life history investment decisions in founding ant queens. Frontiers in Ecology and Evolution, 8, Article 76. https://doi.org/10.3389/fevo.2020.00076

Pratama, A. A., Javier Jimenez, D., Chen, Q., Bunk, B., Sproeer, C., Overmann, J., & van Elsas, J. D. (2020). Delineation of a subgroup of the genus Paraburkholderia, including P. terrae DSM 17804(T), P. hospita DSM 17164(T), and four soil-isolated fungiphiles, reveals remarkable genomic and ecological features: Proposal for the definition of a P. hospita species cluster. Genome Biology and Evolution, 12(4), 325-344. https://doi.org/10.1093/gbe/evaa031

Jimenez, D. J., Wang, Y., Chaib de Mares, M., Cortes-Tolalpa, L., Mertens, J. A., Hector, R. E., Lin, J., Johnson, J., Lipzen, A., Barry, K., Mondo, S. J., Grigoriev, I., Nichols, N. N., & van Elsas, J. D. (2020). Defining the eco-enzymological role of the fungal strain Coniochaeta sp. 2T2.1 in a tripartite lignocellulolytic microbial consortium. FEMS microbiology ecology, 96(1), Article 186. https://doi.org/10.1093/femsec/fiz186

Puentes-Tellez, P. E., & Salles, J. F. (2020). Dynamics of abundant and rare bacteria during degradation of lignocellulose from sugarcane biomass. Microbial ecology, 79(2), 312-325. https://doi.org/10.1007/s00248-019-01403-w

Dietz, M. W., Salles, J. F., Hsu, B.-Y., Dijkstra, C., Groothuis, T. G. G., van der Velde, M., Verkuil, Y. I., & Tieleman, B. I. (2020). Prenatal transfer of gut bacteria in Rock pigeon. Microorganisms, 8(1), Article 61. https://doi.org/10.3390/microorganisms8010061

Kyselkova, M., Salles, J. F., Dumestre, A., Benoit, Y., & Grundmann, G. L. (2019). Distinct bacterial consortia established in ETBE-degrading enrichments from a polluted aquifer. Applied Sciences, 9(20). https://doi.org/10.3390/app9204247

Brinker, P., Fontaine, M. C., Beukeboom, L. W., & Salles, J. F. (2019). Host, symbionts, and the microbiome: The missing tripartite interaction. Trends in Microbiology, 27(6), 480-488. https://doi.org/10.1016/j.tim.2019.02.002

Xing, J., Wang, H., Brookes, P. C., Salles, J. F., & Xu, J. (2019). Soil pH and microbial diversity constrain the survival of E-coli in soil. Soil biology & biochemistry, 128, 139-149. https://doi.org/10.1016/j.soilbio.2018.10.013

Pires, E. S., Pires Hardoim, C. C., Miranda, K. R., Secco, D. A., Lobo, L. A., de Carvalho, D. P., Han, J., Borchers, C. H., Ferreira, R. B. R., Salles, J. F., Cavalcanti Pilotto Domingues, R. M., & Martha Antunes, L. C. (2019). The gut microbiome and metabolome of two riparian communities in the Amazon. Frontiers in Microbiology, 10, Article 2003. https://doi.org/10.3389/fmicb.2019.02003

van der Loos, L. M., Eriksson, B. K., & Falcão Salles, J. (2019). The Macroalgal Holobiont in a Changing Sea. Trends in Microbiology, 27(7), 635-650. https://doi.org/10.1016/j.tim.2019.03.002

Gurung, K., Wertheim, B., & Salles, J. F. (2019). The microbiome of pest insects: It is not just bacteria. Entomologia Experimentalis et Applicata, 167(3), 156-170. https://doi.org/10.1111/eea.12768

van Ginkel, W. G., van Vliet, D., van der Goot, E., Faassen, M. H. J. R., Vogel, A., Heiner-Fokkema, M. R., van der Zee, E. A., & van Spronsen, F. J. (2019). Blood and brain biochemistry and behaviour in NTBC and dietary treated tyrosinemia type 1 mice. Nutrients, 11(10), Article 2486. https://doi.org/10.3390/nu11102486

Bruinenberg, V. M., van Vliet, D., van der Goot, E., Counotte, D. S., Kuhn, M., van Spronsen, F. J., & van der Zee, E. A. (2019). Long-term dietary intervention with low Phe and/or a specific nutrient combination improve certain aspects of brain functioning in phenylketonuria (PKU). PLoS ONE, 14(3), Article 0213391. https://doi.org/10.1371/journal.pone.0213391

van Vliet, D., van der Goot, E., van Ginkel, W. G., van Faassen, M. H. J. R., de Blaauw, P., Kema, I. P., Martinez, A., Heiner-Fokkema, M. R., van der Zee, E. A., & van Spronsen, F. J. (2019). The benefit of large neutral amino acid supplementation to a liberalized phenylalanine-restricted diet in adult phenylketonuria patients: Evidence from adult Pah-Enu2 mice. Nutrients, 11(9), Article 2252. https://doi.org/10.3390/nu11092252

Jia, X., Dini-Andreote, F., & Salles, J. F. (2018). Community assembly processes of the microbial rare biosphere. Trends in Microbiology, 26(9), 738-747. https://doi.org/10.1016/j.tim.2018.02.011

Wang, M., Veldsink, J. H., Dini-Andreote, F., & Salles, J. F. (2018). Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 111(11), 2061-2078. https://doi.org/10.1007/s10482-018-1098-5

Puentes-Tellez, P. E., & Salles, J. F. (2018). Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. Microbial ecology, 76(2), 419-429. https://doi.org/10.1007/s00248-017-1141-5

Leite, D. C. A., Salles, J. F., Calderon, E. N., Castro, C. B., Bianchini, A., Marques, J. A., van Elsas, J. D., & Peixoto, R. S. (2018). Coral bacterial-core abundance and network complexity as proxies for anthropogenic pollution. Frontiers in Microbiology, 9, Article 833. https://doi.org/10.3389/fmicb.2018.00833

Dini-Andreote, F., van Elsas, J. D., Olff, H., & Salles, J. F. (2018). Dispersal-competition tradeoff in microbiomes in the quest for land colonization. Scientific Reports, 8(1), Article 9451. https://doi.org/10.1038/s41598-018-27783-6

Cortes-Tolalpa, L., Norder, J., van Elsas, J. D., & Falcao Salles, J. (2018). Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Applied Microbiology and Biotechnology, 2913-2927. https://doi.org/10.1007/s00253-017-8714-6

van Veelen, H. P. J., Salles, J. F., & Tieleman, B. I. (2018). Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. The ISME journal, 12(5), 1375-1388. https://doi.org/10.1038/s41396-018-0067-3

Mas-Carrio, E., Dini-Andreote, F., Brossi, M. J. D. L., Salles, J. F., & Olff, H. (2018). Organic amendment under increasing agricultural intensification: Effects on soil bacterial communities and plant productivity. Frontiers in Microbiology, 9, Article 2612. https://doi.org/10.3389/fmicb.2018.02612

Nunes, I., Jurburg, S., Jacquiod, S., Brejnrod, A., Salles, J. F., Prieme, A., & Sorensen, S. J. (2018). Soil bacteria show different tolerance ranges to an unprecedented disturbance. Biology and Fertility of Soils, 54(2), 189-202. https://doi.org/10.1007/s00374-017-1255-4

Leite, D. C. A., Salles, J. F., Calderon, E. N., van Elsas, J. D., & Peixoto, R. S. (2018). Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont. Ecology and Evolution, 8(3), 1818-1832. https://doi.org/10.1002/ece3.3717

Javier Jimenez, D., Chaib De Mares, M., & Falcao Salles, J. (2018). Temporal expression dynamics of plant biomass-degrading enzymes by a synthetic bacterial consortium growing on sugarcane bagasse. Frontiers in Microbiology, 9, Article 299. https://doi.org/10.3389/fmicb.2018.00299

Mallon, C. A., Roux, X. L., Doorn, G. S. V., Dini-Andreote, F., Poly, F., & Salles, J. F. (2018). The impact of failure: Unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche. The ISME journal, 12(3), 728-741. https://doi.org/10.1038/s41396-017-0003-y

Brinker, P., Weig, A., Rambold, G., Feldhaar, H., & Tragust, S. (2019). Microbial community composition of nest-carton and adjoining soil of the ant Lasius fuliginosus and the role of host secretions in structuring microbial communities. Fungal Ecology, 38, 44-53. https://doi.org/10.1016/j.funeco.2018.08.007

van der Goot, E., Bruinenberg, V. M., Hormann, F. M., Eisel, U. L. M., van Spronsen, F. J., & van der Zee, E. A. (2019). Hippocampal microglia modifications in C57Bl/6 Pah^enu2 and BTBR Pah^enu2 phenylketonuria (PKU) mice depend on the genetic background, irrespective of disturbed sleep patterns. Neurobiology of Learning and Memory, 160, 139-143. https://doi.org/10.1016/j.nlm.2018.05.002

van Vliet, D., van der Goot, E., Bruinenberg, V. M., van Faassen, M., de Blaauw, P., Kema, I. P., Heiner-Fokkema, M. R., van der Zee, E. A., & van Spronsen, F. J. (2018). Large neutral amino acid supplementation as an alternative to the phenylalanine-restricted diet in adults with phenylketonuria: Evidence from adult Pah-enu2 mice. Journal of Nutritional Biochemistry, 53, 20-27. https://doi.org/10.1016/j.jnutbio.2017.09.020

Jurburg, S. D., Natal-da-Luz, T., Raimundo, J., Morais, P. V., Sousa, J. P., van Elsas, J. D., & Salles, J. F. (2018). Bacterial communities in soil become sensitive to drought under intensive grazing. Science of the Total Environment, 618, 1638-1646. https://doi.org/10.1016/j.scitotenv.2017.10.012

Jurburg, S. D., Nunes, I., Stegen, J. C., Le Roux, X., Priemé, A., Sørensen, S. J., & Salles, J. F. (2017). Autogenic succession and deterministic recovery following disturbance in soil bacterial communities. Scientific Reports, 7, Article 45691. https://doi.org/10.1038/srep45691

Cortes Tolalpa, L., Falcao Salles, J., & van Elsas, J. (2017). Bacterial synergism in lignocellulose biomass degradation: Complementary roles of degraders as influenced by complexity of the carbon source. Frontiers in Microbiology, 8, Article 1628. https://doi.org/10.3389/fmicb.2017.01628

López-Lozano, N. E., Pereira E Silva, M. C., Poly, F., Guillaumaud, N., van Elsas, J. D., & Salles, J. F. (2017). Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils. Antonie Van Leeuwenhoek: International Journal of General and Molecular Microbiology, 110(11), 1453-1465. https://doi.org/10.1007/s10482-017-0898-3

Javier Jiménez, D., Dini-Andreote, F., DeAngelis, K. M., Singer, S. W., Salles, J. F., & van Elsas, J. D. (2017). Ecological insights into the dynamics of plant biomass-degrading microbial consortia. Trends in Microbiology, 25(10), 788-796. https://doi.org/10.1016/j.tim.2017.05.012

Wang, M., Li, E., Liu, C., Jousset, A., & Salles, J. F. (2017). Functionality of root-associated bacteria along a salt marsh primary succession. Frontiers in Microbiology, 8, Article 2102. https://doi.org/10.3389/fmicb.2017.02102

Jurburg, S. D., Nunes, I., Brejnrod, A., Jacquiod, S., Prieme, A., Sorensen, S. J., Van Elsas, J. D., & Salles, J. F. (2017). Legacy effects on the recovery of soil bacterial communities from extreme temperature perturbation. Frontiers in Microbiology, 8, Article 1832. https://doi.org/10.3389/fmicb.2017.01832

Tilstra, A., Wijgerde, T., Dini-Andreote, F., Eriksson, B. K., Salles, J. F., Pen, I., Osinga, R., & Wild, C. (2017). Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata. PeerJ, 5, Article e3802. https://doi.org/10.7717/peerj.3802

Vink, S. N., Jordan, N. R., Aldrich-Wolfe, L., Huerd, S. C., Sheaffer, C. C., & Kinkel, L. L. (2017). Soil conditioning affects interactions between native and invasive exotic perennials of semi-natural grasslands. Journal of Applied Ecology, 54, 1526-1533. https://doi.org/10.1111/1365-2664.12823

Zhang, M., Brons, J. K., & van Elsas, J. D. (2016). The complete sequences and ecological roles of two IncP-1 beta plasmids, pHB44 and pBS64, isolated from the mycosphere of Laccaria proxima. Frontiers in Microbiology, 7, Article 909. https://doi.org/10.3389/fmicb.2016.00909

Bruinenberg, V. M., van der Goot, E., van Vliet, D., de Groot, M. J., Mazzola, P. N., Heiner-Fokkema, M. R., van Faassen, M., van Spronsen, F. J., & van der Zee, E. A. (2016). The behavioral consequence of phenylketonuria in mice depends on the genetic background. Frontiers in Behavioral Neuroscience, 10(233), Article 233. https://doi.org/10.3389/fnbeh.2016.00233

Vink, S. N., Jordan, N. R., Huerd, S. C., Sheaffer, C. C., Kinkel, L. L., & Aldrich-Wolfe, L. (2015). Soil conditioning effects of native and exotic grassland perennials on the establishment of native and exotic plants. Plant and Soil, 393, 335-349. https://doi.org/10.1007/s11104-015-2498-1

Zhang, M., Warmink, J., Pereira e Silva, M. C., Brons, J., Smalla, K., & van Elsas, J. D. (2015). IncP-1 beta Plasmids Are Important Carriers of Fitness Traits for Variovorax Species in the Mycosphere-Two Novel Plasmids, pHB44 and pBS64, with Differential Effects Unveiled. Microbial ecology, 70(1), 141-153. https://doi.org/10.1007/s00248-014-0550-y

Vink, S. N., Neilson, R., Robinson, D., & Daniell, T. (2014). Temporal and land use effects on soil bacterial community structure of the machair, an EU Habitats Directive Annex I low-input agricultural system. Applied Soil Ecology, 73, 116-123. https://doi.org/10.1016/j.apsoil.2013.08.012

Coyer, J. A., Hoarau, G., Kuo, J., Tronholm, A., Veldsink, J., & Olsen, J. L. (2013). Phylogeny and temporal divergence of the seagrass family Zosteraceae using one nuclear and three chloroplast loci. Systematics and biodiversity, 11(3), 271-284. https://doi.org/10.1080/14772000.2013.821187

Brons, J., & van Elsas, J. D. (2008). Analysis of bacterial communities in soil by use of denaturing gradient gel electrophoresis and clone libraries, as influenced by different reverse primers. Applied Environmental Microbiology, 74(9), 2717-2727. https://doi.org/10.1128/AEM.02195-07

Coyer, J. A., Miller, K. A., Engle, J. M., Veldsink, J., Cabello-Pasini, A., Stam, W. T., & Olsen, J. L. (2008). Eelgrass Meadows in the California Channel Islands and Adjacent Coast Reveal a Mosaic of Two Species, Evidence for Introgression and Variable Clonality. Annals of Botany, 101(1), 73-87. https://doi.org/10.1093/aob/mcm288

Hoarau, G. G., Coyer, J. A., Veldsink, J. H., Stam, W. T., & Olsen, J. L. (2007). Glacial refugia and recolonization pathways in the brown seaweed Fucus serratus. Molecular Ecology, 16(17), 3606-3616. https://doi.org/10.1111/j.1365-294x.2007.03408.x

Olsen, JL., Stam, WT., Coyer, JA., Reusch, TBH., Billingham, M., Bostrom, C., Calvert, E., Christie, H., Granger, S., La Lumiere, R., Milchakova, N., Oudot-Le Secq, MP., Procaccini, G., Sanjabi, B., Serrao, E., Veldsink, J., Widdicombe, S., & Wyllie-Echeverria, S. (2004). North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L. Molecular Ecology, 13(7), 1923-1941. https://doi.org/10.1111/j.1365-294X.2004.02205.x

Olsen, JL., Sadowski, G., Stam, WT., Veldsink, JH., & Jones, K. (2002). Characterization of microsatellite loci in the marine seaweed Ascophyllum nodosum (Phaeophyceae; Fucales). Molecular Ecology Notes, 2(1), 33-34. https://doi.org/10.1046/j.1471-8286.2002.00137.x

Coyer, J. A., Veldsink, J. H., Jones, K., Stam, W. T., & Olsen, J. L. (2002). Characterization of microsatellite loci in the marine seaweeds, Fucus serratus and F-evanescens (Heterokontophyta; Fucaceae). Molecular Ecology Notes, 2(1), 35-37. https://doi.org/10.1046/j.1471-8286.2002.00138.x

Schaafsma, A., van Doormaal, J. J., Muskiet, F. A. J., Hofstede, G. J. H., Pakan, I., & van der Veer, E. (2002). Positive effects of a chicken eggshell powder-enriched vitamin-mineral supplement on femoral neck bone mineral density in healthy late post-menopausal Dutch women. British Journal of Nutrition, 87(3), 267-275. https://doi.org/10.1079/BJN2001515

Daemen, T., Hofstede, G., Ten Kate, M. T., Bakker-Woudenberg, I. A. J. M., & Scherphof, G. L. (1995). Liposomal doxorubicin-induced toxicity: Depletion and impairment of phagocytic activity of liver macrophages. International Journal of Cancer, 61(5), 716-721. https://doi.org/10.1002/ijc.2910610520