Research group

Amplicon Sequencing, Bioinformatics Infrastructure, Biological Databases, Data Visualization, Genome Assembly, Genome Sequencing, Genomic Annotation, Genomics, Metagenomics, Metatranscriptomics, Microbial communities, Non-model organisms, Phylogenetic Analysis, RNA Sequencing (RNA-seq), Single-cell (scRNA-seq), Single-cell omics, Transcriptomics

Bonacolta, A. M., Weiler, B. A., Grimes, C. J., Trznadel, M., Vermeij, M. J. A., Keeling, P. J., & del Campo, J. (2025). Fireworms are a reservoir and potential vector for coral-infecting apicomplexans. The ISME Journal, 19(1). https://doi.org/10.1093/ismejo/wraf078

Bonacolta, A. M., Krause‐Massaguer, J., Unuma, T., & del Campo, J. (2025). The Sea Cucumber‐Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine‐Host‐Specific Clade of Apicomplexans. Journal of Eukaryotic Microbiology, 72(3). Portico. https://doi.org/10.1111/jeu.70013

Bonacolta, A. M., Weiler, B. A., Porta-Fitó, T., Sweet, M., Keeling, P., & del Campo, J. (2023). Beyond the Symbiodiniaceae: diversity and role of microeukaryotic coral symbionts. Coral Reefs, 42(2), 567–577. https://doi.org/10.1007/s00338-023-02352-0

Rosales, S. M., Huebner, L. K., Evans, J. S., Apprill, A., Baker, A. C., Bellantuono, A. J., Brandt, M. E., Clark, A. S., del Campo, J., Dennison, C. E., Huntley, N. E., Kellogg, C. A., Medina, M., Meyer, J. L., Muller, E. M., Rodriguez-Lanetty, M., Salerno, J. L., Schill, W. B., Shilling, E. N., … Voss, J. D. (2022). A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in lesions and unaffected tissue of diseased colonies. https://doi.org/10.1101/2022.09.30.510359

Bonacolta, A. M., Miravall, J., Gómez-Gras, D., Ledoux, J.-B., López-Sendino, P., Garrabou, J., Massana, R., & del Campo, J. (2022). Apicomplexans predict thermal stress mortality in the Mediterranean coralParamuricea clavata. https://doi.org/10.1101/2022.11.23.517658

Orkin, J. D., Montague, M. J., Tejada-Martinez, D., de Manuel, M., del Campo, J., Cheves Hernandez, S., Di Fiore, A., Fontsere, C., Hodgson, J. A., Janiak, M. C., Kuderna, L. F. K., Lizano, E., Martin, M. P., Niimura, Y., Perry, G. H., Valverde, C. S., Tang, J., Warren, W. C., de Magalhães, J. P., … Melin, A. D. (2021). The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proceedings of the National Academy of Sciences, 118(7). https://doi.org/10.1073/pnas.2010632118

Bonacolta, A. M., Connelly, M. T., Rosales, S., del Campo, J., & Traylor-Knowles, N. (2020). The Starlet Sea Anemone,Nematostella vectensis, possesses body region-specific bacterial associations with spirochetes dominating the capitulum. https://doi.org/10.1101/2020.05.10.084863

Weiler, B. A., Sà, E. L., Sieracki, M. E., Massana, R., & del Campo, J. (2020). Mediocremonas mediterraneus, a New Member within the Developea. https://doi.org/10.1101/2020.05.12.090621

Bass, D., & del Campo, J. (2020). Microeukaryotes in animal and plant microbiomes: Ecologies of disease? European Journal of Protistology, 76, 125719. https://doi.org/10.1016/j.ejop.2020.125719

del Campo, J., Pons, M. J., Herranz, M., Wakeman, K. C., del Valle, J., Vermeij, M. J. A., Leander, B. S., & Keeling, P. J. (2019). Validation of a universal set of primers to study animal‐associated microeukaryotic communities. Environmental Microbiology, 21(10), 3855–3861. Portico. https://doi.org/10.1111/1462-2920.14733

del Campo, J., Bass, D., & Keeling, P. J. (2019). The eukaryome: Diversity and role of microeukaryotic organisms associated with animal hosts. Functional Ecology, 34(10), 2045–2054. Portico. https://doi.org/10.1111/1365-2435.13490

López-Escardó, D., Paps, J., de Vargas, C., Massana, R., Ruiz-Trillo, I., & del Campo, J. (2018). Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity. https://doi.org/10.1101/253146

Orsi, W. D., Wilken, S., del Campo, J., Heger, T., James, E., Richards, T. A., Keeling, P. J., Worden, A. Z., & Santoro, A. E. (2018). Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. Environmental Microbiology, 20(2), 815–827. Portico. https://doi.org/10.1111/1462-2920.14018

Heger, T. J., Giesbrecht, I. J. W., Gustavsen, J., del Campo, J., Kellogg, C. T. E., Hoffman, K. M., Lertzman, K., Mohn, W. W., & Keeling, P. J. (2018). High‐throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity. Environmental Microbiology, 20(3), 1185–1203. Portico. https://doi.org/10.1111/1462-2920.14061

del Campo, J., Kolisko, M., Boscaro, V., Santoferrara, L. F., Nenarokov, S., Massana, R., Guillou, L., Simpson, A., Berney, C., de Vargas, C., Brown, M. W., Keeling, P. J., & Wegener Parfrey, L. (2018). EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology, 16(9), e2005849. https://doi.org/10.1371/journal.pbio.2005849

Orkin, J. D., Montague, M. J., Tejada-Martinez, D., de Manuel, M., del Campo, J., Hernandez, S. C., Di Fiore, A., Fontsere, C., Hodgson, J. A., Janiak, M. C., Kuderna, L. F. K., Lizano, E., Martin, M. P., Niimura, Y., Perry, G. H., Valverde, C. S., Tang, J., Warren, W. C., de Magalhães, J. P., … Melin, A. D. (2018). The evolution of ecological flexibility, large brains, and long lives: capuchin monkey genomics revealed with fecalFACS. https://doi.org/10.1101/366112

Freeman, M. A., Fuss, J., Kristmundsson, Á., Bjorbækmo, M. F. M., Mangot, J.-F., del Campo, J., Keeling, P. J., Shalchian-Tabrizi, K., & Bass, D. (2017). X-Cells Are Globally Distributed, Genetically Divergent Fish Parasites Related to Perkinsids and Dinoflagellates. Current Biology, 27(11), 1645-1651.e3. https://doi.org/10.1016/j.cub.2017.04.045

Knowles, B., Bailey, B., Boling, L., Breitbart, M., Cobián-Güemes, A., del Campo, J., Edwards, R., Felts, B., Grasis, J., Haas, A. F., Katira, P., Kelly, L. W., Luque, A., Nulton, J., Paul, L., Peters, G., Robinett, N., Sandin, S., Segall, A., … Rohwer, F. (2017). Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature Microbiology, 2(7). https://doi.org/10.1038/nmicrobiol.2017.64

Berney, C., Ciuprina, A., Bender, S., Brodie, J., Edgcomb, V., Kim, E., Rajan, J., Parfrey, L. W., Adl, S., Audic, S., Bass, D., Caron, D. A., Cochrane, G., Czech, L., Dunthorn, M., Geisen, S., Glöckner, F. O., Mahé, F., Quast, C., … de Vargas, C. (2017). UniEuk: Time to Speak a Common Language in Protistology! Journal of Eukaryotic Microbiology, 64(3), 407–411. Portico. https://doi.org/10.1111/jeu.12414

del Campo, J., James, E. R., Hirakawa, Y., Fiorito, R., Kolisko, M., Irwin, N. A. T., Mathur, V., Boscaro, V., Hehenberger, E., Karnkowska, A., Scheffrahn, R. H., & Keeling, P. J. (2017). Pseudotrichonympha leei, Pseudotrichonympha lifesoni, and Pseudotrichonympha pearti, new species of parabasalian flagellates and the description of a rotating subcellular structure. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-16259-8

Hehenberger, E., Tikhonenkov, D. V., Kolisko, M., del Campo, J., Esaulov, A. S., Mylnikov, A. P., & Keeling, P. J. (2017). Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals. Current Biology, 27(13), 2043-2050.e6. https://doi.org/10.1016/j.cub.2017.06.006

Boscaro, V., James, E. R., Fiorito, R., Hehenberger, E., Karnkowska, A., del Campo, J., Kolisko, M., Irwin, N. A. T., Mathur, V., Scheffrahn, R. H., & Keeling, P. J. (2017). Molecular characterization and phylogeny of four new species of the genus Trichonympha (Parabasalia, Trichonymphea) from lower termite hindguts. International Journal of Systematic and Evolutionary Microbiology, 67(9), 3570–3575. https://doi.org/10.1099/ijsem.0.002169

Keeling, P. J., & Campo, J. del. (2017). Marine Protists Are Not Just Big Bacteria. Current Biology, 27(11), R541–R549. https://doi.org/10.1016/j.cub.2017.03.075

Hehenberger, E., James, E. R., del Campo, J., Buckland‐Nicks, J. A., Reimchen, T. E., & Keeling, P. J. (2017). Fish Parasite Dinoflagellates Haidadinium ichthyophilum and Piscinoodinium Share a Recent Common Ancestor. Journal of Eukaryotic Microbiology, 65(1), 127–131. Portico. https://doi.org/10.1111/jeu.12430

Strassert, J. F. H., Karnkowska, A., Hehenberger, E., del Campo, J., Kolisko, M., Okamoto, N., Burki, F., Janouškovec, J., Poirier, C., Leonard, G., Hallam, S. J., Richards, T. A., Worden, A. Z., Santoro, A. E., & Keeling, P. J. (2017). Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. The ISME Journal, 12(1), 304–308. https://doi.org/10.1038/ismej.2017.167

Gawryluk, R. M. R., del Campo, J., Okamoto, N., Strassert, J. F. H., Lukeš, J., Richards, T. A., Worden, A. Z., Santoro, A. E., & Keeling, P. J. (2016). Morphological Identification and Single-Cell Genomics of Marine Diplonemids. Current Biology, 26(22), 3053–3059. https://doi.org/10.1016/j.cub.2016.09.013

del Campo, J., Guillou, L., Hehenberger, E., Logares, R., López-García, P., & Massana, R. (2016). Ecological and evolutionary significance of novel protist lineages. European Journal of Protistology, 55, 4–11. https://doi.org/10.1016/j.ejop.2016.02.002

del Campo, J., Pombert, J.-F., Šlapeta, J., Larkum, A., & Keeling, P. J. (2016). The ‘other’ coral symbiont: Ostreobium diversity and distribution. The ISME Journal, 11(1), 296–299. https://doi.org/10.1038/ismej.2016.101

Pan, J., del Campo, J., & Keeling, P. J. (2016). Reference Tree and Environmental Sequence Diversity of Labyrinthulomycetes. Journal of Eukaryotic Microbiology, 64(1), 88–96. Portico. https://doi.org/10.1111/jeu.12342

Woo, Y. H., Ansari, H., Otto, T. D., Klinger, C. M., Kolisko, M., Michálek, J., Saxena, A., Shanmugam, D., Tayyrov, A., Veluchamy, A., Ali, S., Bernal, A., del Campo, J., Cihlář, J., Flegontov, P., Gornik, S. G., Hajdušková, E., Horák, A., Janouškovec, J., … Pain, A. (2015). Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. ELife, 4. CLOCKSS. https://doi.org/10.7554/elife.06974

Torruella, G., de Mendoza, A., Grau-Bové, X., Antó, M., Chaplin, M. A., del Campo, J., Eme, L., Pérez-Cordón, G., Whipps, C. M., Nichols, K. M., Paley, R., Roger, A. J., Sitjà-Bobadilla, A., Donachie, S., & Ruiz-Trillo, I. (2015). Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi. Current Biology, 25(18), 2404–2410. https://doi.org/10.1016/j.cub.2015.07.053

Richards, T. A., Leonard, G., Mahé, F., del Campo, J., Romac, S., Jones, M. D. M., Maguire, F., Dunthorn, M., De Vargas, C., Massana, R., & Chambouvet, A. (2015). Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proceedings of the Royal Society B: Biological Sciences, 282(1819), 20152243. https://doi.org/10.1098/rspb.2015.2243

del Campo, J., Mallo, D., Massana, R., de Vargas, C., Richards, T. A., & Ruiz‐Trillo, I. (2015). Diversity and distribution of unicellular opisthokonts along the <scp>E</scp>uropean coast analysed using high‐throughput sequencing. Environmental Microbiology, 17(9), 3195–3207. Portico. https://doi.org/10.1111/1462-2920.12759

del Campo, J., Sieracki, M. E., Molestina, R., Keeling, P., Massana, R., & Ruiz-Trillo, I. (2014). The others: our biased perspective of eukaryotic genomes. Trends in Ecology & Evolution, 29(5), 252–259. https://doi.org/10.1016/j.tree.2014.03.006

Sebé-Pedrós, A., Irimia, M., del Campo, J., Parra-Acero, H., Russ, C., Nusbaum, C., Blencowe, B. J., & Ruiz-Trillo, I. (2013). Regulated aggregative multicellularity in a close unicellular relative of metazoa. ELife, 2. CLOCKSS. https://doi.org/10.7554/elife.01287

del Campo, J., & Ruiz-Trillo, I. (2013). Environmental Survey Meta-analysis Reveals Hidden Diversity among Unicellular Opisthokonts. Molecular Biology and Evolution, 30(4), 802–805. https://doi.org/10.1093/molbev/mst006

del Campo, J., Balagué, V., Forn, I., Lekunberri, I., & Massana, R. (2013). Culturing Bias in Marine Heterotrophic Flagellates Analyzed Through Seawater Enrichment Incubations. Microbial Ecology, 66(3), 489–499. https://doi.org/10.1007/s00248-013-0251-y

Roldán, M., Ramírez, M., del Campo, J., Hernández-Mariné, M., & Komárek, J. (2013). Chalicogloea cavernicola gen. nov., sp. nov. (Chroococcales, Cyanobacteria ), from low-light aerophytic environments: combined molecular, phenotypic and ecological criteria. International Journal of Systematic and Evolutionary Microbiology, 63(Pt_6), 2326–2333. https://doi.org/10.1099/ijs.0.045468-0

Massana, R., del Campo, J., Sieracki, M. E., Audic, S., & Logares, R. (2013). Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. The ISME Journal, 8(4), 854–866. https://doi.org/10.1038/ismej.2013.204

Weber, F., del Campo, J., Wylezich, C., Massana, R., & Jürgens, K. (2012). Unveiling Trophic Functions of Uncultured Protist Taxa by Incubation Experiments in the Brackish Baltic Sea. PLoS ONE, 7(7), e41970. https://doi.org/10.1371/journal.pone.0041970

Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C., Burgaud, G., de Vargas, C., Decelle, J., del Campo, J., Dolan, J. R., Dunthorn, M., Edvardsen, B., Holzmann, M., Kooistra, W. H. C. F., Lara, E., Le Bescot, N., Logares, R., … Christen, R. (2012). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41(D1), D597–D604. https://doi.org/10.1093/nar/gks1160

del Campo, J., Not, F., Forn, I., Sieracki, M. E., & Massana, R. (2012). Taming the smallest predators of the oceans. The ISME Journal, 7(2), 351–358. https://doi.org/10.1038/ismej.2012.85

del Campo, J., & Massana, R. (2011). Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys. Protist, 162(3), 435–448. https://doi.org/10.1016/j.protis.2010.10.003

Villanueva, L., del Campo, J., Guerrero, R., & Geyer, R. (2010). Intact Phospholipid and Quinone Biomarkers to Assess Microbial Diversity and Redox State in Microbial Mats. Microbial Ecology, 60(1), 226–238. https://doi.org/10.1007/s00248-010-9645-2

Villanueva, L., Del Campo, J., & Guerrero, R. (2010). Diversity and physiology of polyhydroxyalkanoate-producing and -degrading strains in microbial mats. FEMS Microbiology Ecology, 74(1), 42–54. https://doi.org/10.1111/j.1574-6941.2010.00928.x

Massana, R., Pernice, M., Bunge, J. A., & del Campo, J. (2010). Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean. The ISME Journal, 5(2), 184–195. https://doi.org/10.1038/ismej.2010.104

Not, F., del Campo, J., Balagué, V., de Vargas, C., & Massana, R. (2009). New Insights into the Diversity of Marine Picoeukaryotes. PLoS ONE, 4(9), e7143. https://doi.org/10.1371/journal.pone.0007143

Rodríguez‐Martínez, R., Labrenz, M., Del Campo, J., Forn, I., Jürgens, K., & Massana, R. (2009). Distribution of the uncultured protist MAST‐4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real‐time quantitative PCR. Environmental Microbiology, 11(2), 397–408. Portico. https://doi.org/10.1111/j.1462-2920.2008.01779.x

González, J. M., Fernández-Gómez, B., Fernàndez-Guerra, A., Gómez-Consarnau, L., Sánchez, O., Coll-Lladó, M., del Campo, J., Escudero, L., Rodríguez-Martínez, R., Alonso-Sáez, L., Latasa, M., Paulsen, I., Nedashkovskaya, O., Lekunberri, I., Pinhassi, J., & Pedrós-Alió, C. (2008). Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria). Proceedings of the National Academy of Sciences, 105(25), 8724–8729. https://doi.org/10.1073/pnas.0712027105

Massana, R., Del Campo, J., Dinter, C., & Sommaruga, R. (2007). Crash of a population of the marine heterotrophic flagellate Cafeteria roenbergensis by viral infection. Environmental Microbiology, 9(11), 2660–2669. Portico. https://doi.org/10.1111/j.1462-2920.2007.01378.x