del Campo J., Kolisko M., Boscaro V., Santoferrara LF., Nenarokov S., Massana R., Guillou L., Simpson A., Berney C., de Vargas C., Brown MW., Keeling PJ., Wegener Parfrey L. 2018. EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology 16:e2005849. DOI: 10.1371/journal.pbio.2005849.

Number of papers citing EukRef: 57


Cahoon, A. and R. VanGundy (2022). “Alveolates (dinoflagellates, ciliates and apicomplexans) and Rhizarians are the most common microbial eukaryotes in temperate Appalachian karst caves”. In: Environmental Microbiology Reports 14.4, pp. 538-548. DOI: 10.1111/1758-2229.13060.

Caracciolo, M., F. Rigaut-Jalabert, S. Romac, et al. (2022). “Seasonal dynamics of marine protist communities in tidally mixed coastal waters”. In: Molecular Ecology 31.14, pp. 3761-3783. DOI: 10.1111/mec.16539.

Cho, A., D. Tikhonenkov, E. Hehenberger, et al. (2022). “Monophyly of diverse Bigyromonadea and their impact on phylogenomic relationships within stramenopiles”. In: Molecular Phylogenetics and Evolution 171. DOI: 10.1016/j.ympev.2022.107468.

Duerschlag, J., W. Mohr, T. Ferdelman, et al. (2022). “Niche partitioning by photosynthetic plankton as a driver of CO2-fixation across the oligotrophic South Pacific Subtropical Ocean”. In: ISME Journal 16.2, pp. 465-476. DOI: 10.1038/s41396-021-01072-z.

Eshghi Sahraei, S., B. Furneaux, K. Kluting, et al. (2022). “Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding”. In: Ecology and Evolution 12.3. DOI: 10.1002/ece3.8676.

Frantal, D., S. Agatha, D. Beisser, et al. (2022). “Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.787290.

Igai, K., O. Kitade, J. Fu, et al. (2022). “Fine-scale genetic diversity and putative ecotypes of oxymonad protists coinhabiting the hindgut of Reticulitermes speratus”. In: Molecular Ecology 31.4, pp. 1317-1331. DOI: 10.1111/mec.16309.

Metz, S., P. Huber, V. Accattatis, et al. (2022). “Freshwater protists: unveiling the unexplored in a large floodplain system”. In: Environmental Microbiology 24.4, pp. 1731-1745. DOI: 10.1111/1462-2920.15838.

Panova, M., M. Varfolomeeva, E. Gafarova, et al. (2022). “First insights into the gut microbiomes and the diet of the Littorina snail ecotypes, a recently emerged marine evolutionary model”. In: Evolutionary Applications. DOI: 10.1111/eva.13447.

Reid, B., J. Servis, M. Timmers, et al. (2022). “18S rDNA amplicon sequence data (V1-V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific”. In: Metabarcoding and Metagenomics 6, pp. 89-99. DOI: 10.3897/mbmg.6.78762.

Sandin, M., S. Romac, and F. Not (2022). “Intra-genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing”. In: Environmental Microbiology 24.7, pp. 2979-2993. DOI: 10.1111/1462-2920.16081.

Tikhonenkov, D., M. Jamy, A. Borodina, et al. (2022). “On the origin of TSAR: Morphology, diversity and phylogeny of Telonemia”. In: Open Biology 12.3. DOI: 10.1098/rsob.210325.

Zafeiropoulos, H., S. Paragkamian, S. Ninidakis, et al. (2022). “PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types”. In: Microorganisms 10.2. DOI: 10.3390/microorganisms10020293.


Burki, F., M. Sandin, and M. Jamy (2021). “Diversity and ecology of protists revealed by metabarcoding”. In: Current Biology 31.19, pp. R1267-R1280. DOI: 10.1016/j.cub.2021.07.066.

Canino, A., A. Bouchez, C. Laplace-Treyture, et al. (2021). “Phytool, a ShinyApp to homogenise taxonomy of freshwater microalgae from DNA barcodes and microscopic observations”. In: Metabarcoding and Metagenomics 5, pp. 199-205. DOI: 10.3897/mbmg.5.74096.

Díaz-Torres, O., J. de Anda, O. Lugo-Melchor, et al. (2021). “Rapid Changes in the Phytoplankton Community of a Subtropical, Shallow, Hypereutrophic Lake During the Rainy Season”. In: Frontiers in Microbiology 12. DOI: 10.3389/fmicb.2021.617151.

Dias, R., P. de Souza, M. Rossi, et al. (2021). “Ciliates as bioindicators of water quality: A case study in the neotropical region and evidence of phylogenetic signals (18S-rDNA)”. In: Environmental Pollution 268. DOI: 10.1016/j.envpol.2020.115760.

Dumack, K. and M. Bonkowski (2021). “Protists in the plant microbiome: an untapped field of research”. In: Methods in Molecular Biology 2232, pp. 77-84. DOI: 10.1007/978-1-0716-1040-4_8.

Gao, B., L. Chi, Y. Zhu, et al. (2021). “An introduction to next generation sequencing bioinformatic analysis in gut microbiome studies”. In: Biomolecules 11.4. DOI: 10.3390/biom11040530.

Greco, M., R. Morard, and M. Kucera (2021). “Single-cell metabarcoding reveals biotic interactions of the Arctic calcifier Neogloboquadrina pachyderma with the eukaryotic pelagic community”. In: Journal of Plankton Research 43.2, pp. 113-125. DOI: 10.1093/plankt/fbab015.

Lavrinienko, A., T. Jernfors, J. Koskimäki, et al. (2021). “Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?” In: Trends in Microbiology 29.1, pp. 19-27. DOI: 10.1016/j.tim.2020.05.019.

Mann, D., R. Trobajo, S. Sato, et al. (2021). “Ripe for reassessment: A synthesis of available molecular data for the speciose diatom family Bacillariaceae”. In: Molecular Phylogenetics and Evolution 158. DOI: 10.1016/j.ympev.2020.106985.

Martini, S., F. Larras, A. Boyé, et al. (2021). “Functional trait-based approaches as a common framework for aquatic ecologists”. In: Limnology and Oceanography 66.3, pp. 965-994. DOI: 10.1002/lno.11655.

Obertegger, U., M. Pindo, and G. Flaim (2021). “Do inferences about freshwater phytoplankton communities change when based on microscopy or high-throughput sequencing data?” In: Freshwater Biology 66.4, pp. 640-655. DOI: 10.1111/fwb.13667.

Rajter, I. Ewers, N. Graupner, et al. (2021). “Colpodean ciliate phylogeny and reference alignments for phylogenetic placements”. In: European Journal of Protistology 77. DOI: 10.1016/j.ejop.2020.125747.

Regaldo, L., V. Márquez, M. Latorre Rapela, et al. (2021). Prokaryotic and Eukaryotic Diversity in Wastewater Treatment: Phenotypic Characterization, Molecular Techniques, and Bioprospecting , pp. 343-365. DOI: 10.1016/B978-0-12-821881-5.00017-9.

Rimet, F., E. Aylagas, A. Borja, et al. (2021). “Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life”. In: Metabarcoding and Metagenomics 5, pp. 17-33. DOI: 10.3897/mbmg.5.58056.

Schiwitza, S. and F. Nitsche (2021). “A Needle in the Haystack – Mapping Sequences to Morphology Exemplified by the Loricate Choanoflagellate Enibas thessalia sp. nov. (Acanthoecida, Acanthoecidae)”. In: Protist 172.1. DOI: 10.1016/j.protis.2020.125782.

Snyder, R., J. Moss, L. Santoferrara, et al. (2021). “Ciliate microzooplankton from the Northeastern Gulf of Mexico”. In: ICES Journal of Marine Science 78.9, pp. 3356-3371. DOI: 10.1093/icesjms/fsab002.

Tedersoo, L., M. Albertsen, S. Anslan, et al. (2021). “Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology”. In: Applied and Environmental Microbiology 87.17, pp. 1-19. DOI: 10.1128/AEM.00626-21.

Tonjer, L., E. Thoen, L. Morgado, et al. (2021). “Fungal community dynamics across a forest–alpine ecotone”. In: Molecular Ecology 30.19, pp. 4926-4938. DOI: 10.1111/mec.16095.

Walker, L., T. Hoppe, and M. Silliker (2021). Molecular techniques and current research approaches , pp. 195-229. DOI: 10.1016/B978-0-12-824281-0.00006-3.

Zhou, Y., B. Sun, B. Xie, et al. (2021). “Warming reshaped the microbial hierarchical interactions”. In: Global Change Biology 27.24, pp. 6331-6347. DOI: 10.1111/gcb.15891.


Djemiel, C., D. Plassard, S. Terrat, et al. (2020). “µgreen-db: A reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria”. In: Scientific Reports 10.1. DOI: 10.1038/s41598-020-62555-1.

Fawley, M. and K. Fawley (2020). “Identification of eukaryotic microalgal strains”. In: Journal of Applied Phycology 32.5, pp. 2699-2709. DOI: 10.1007/s10811-020-02190-5.

Fiore-Donno, A., T. Richter-Heitmann, and M. Bonkowski (2020). “Contrasting Responses of Protistan Plant Parasites and Phagotrophs to Ecosystems, Land Management and Soil Properties”. In: Frontiers in Microbiology 11. DOI: 10.3389/fmicb.2020.01823.

Gottschling, M., J. Chacón, A. Žerdoner ÄŒalasan, et al. (2020). “Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany)”. In: Freshwater Biology 65.2, pp. 193-208. DOI: 10.1111/fwb.13413.

Irion, S., L. Jardillier, I. Sassenhagen, et al. (2020). “Marked spatiotemporal variations in small phytoplankton structure in contrasted waters of the Southern Ocean (Kerguelen area)”. In: Limnology and Oceanography 65.11, pp. 2835-2852. DOI: 10.1002/lno.11555.

Kolisko, M., O. Flegontova, A. Karnkowska, et al. (2020). “EukRef-excavates: Seven curated SSU ribosomal RNA gene databases”. In: Database 2020. DOI: 10.1093/database/baaa080.

LukeÅ¡ová, S., M. Karlicki, L. Tomečková Hadariová, et al. (2020). “Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments”. In: Environmental Microbiology Reports 12.1, pp. 78-91. DOI: 10.1111/1758-2229.12817.

Mann, A., F. Mazel, M. Lemay, et al. (2020). “Biodiversity of protists and nematodes in the wild nonhuman primate gut”. In: ISME Journal 14.2, pp. 609-622. DOI: 10.1038/s41396-019-0551-4.

Santoferrara, L., F. Burki, S. Filker, et al. (2020). “Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding”. In: Journal of Eukaryotic Microbiology 67.5, pp. 612-622. DOI: 10.1111/jeu.12813.

Tůmová, P., E. Nohýnková, A. Klingl, et al. (2020). “A rapid workflow for the characterization of small numbers of unicellular eukaryotes by using correlative light and electron microscopy”. In: Journal of Microbiological Methods 172. DOI: 10.1016/j.mimet.2020.105888.


Adl, S., D. Bass, C. Lane, et al. (2019). “Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes”. In: Journal of Eukaryotic Microbiology 66.1, pp. 4-119. DOI: 10.1111/jeu.12691.

Caron, D. and S. Hu (2019). “Are We Overestimating Protistan Diversity in Nature?” In: Trends in Microbiology 27.3, pp. 197-205. DOI: 10.1016/j.tim.2018.10.009.

Del Campo, J., T. Heger, R. Rodríguez-Martínez, et al. (2019). “Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework”. In: Frontiers in Microbiology 10.OCT. DOI: 10.3389/fmicb.2019.02373.

Ku, C. and A. Sebé-Pedrós (2019). “Using single-cell transcriptomics to understand functional states and interactions in microbial eukaryotes”. In: Philosophical Transactions of the Royal Society B: Biological Sciences 374.1786. DOI: 10.1098/rstb.2019.0098.

Linard, B., K. Swenson, and F. Pardi (2019). “Rapid alignment-free phylogenetic identification of metagenomic sequences”. In: Bioinformatics 35.18, pp. 3303-3312. DOI: 10.1093/bioinformatics/btz068.

Lutz, S., L. Procházková, L. Benning, et al. (2019). “Evaluating amplicon high–throughput sequencing data of microalgae living in melting snow: Improvements and limitations”. In: Fottea 19.2, pp. 115-131. DOI: 10.5507/fot.2019.003.

Metz, S., D. Singer, I. Domaizon, et al. (2019). “Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches”. In: Environmental Microbiology 21.10, pp. 3885-3895. DOI: 10.1111/1462-2920.14738.

Morard, R., N. Vollmar, M. Greco, et al. (2019). “Unassigned diversity of planktonic foraminifera from environmental sequencing revealed as known but neglected species”. In: PLoS ONE 14.3. DOI: 10.1371/journal.pone.0213936.

PrzyboÅš, E. and S. Tarcz (2019). “Global molecular variation of Paramecium jenningsi complex (Ciliophora, Protista): a starting point for further, detailed biogeography surveys”. In: Systematics and Biodiversity 17.5, pp. 527-539. DOI: 10.1080/14772000.2019.1643424.

Richardson, E. and J. Dacks (2019). “Microbial Eukaryotes in oil sands environments: Heterotrophs in the spotlight”. In: Microorganisms 7.6. DOI: 10.3390/microorganisms7060178.

Rimet, F., E. Gusev, M. Kahlert, et al. (2019). “Diat.barcode, an open-access curated barcode library for diatoms”. In: Scientific Reports 9.1. DOI: 10.1038/s41598-019-51500-6.

Santoferrara, L. (2019). “Current practice in plankton metabarcoding: Optimization and error management”. In: Journal of Plankton Research 41.5, pp. 571-582. DOI: 10.1093/plankt/fbz041.

Yu, Z. and N. Chen (2019). “Emerging trends in red tide and major research progresses [国内外赤潮的叒展趋势与研究热点]”. In: Oceanologia et Limnologia Sinica 50.3, pp. 474-486. DOI: 10.11693/hyhz20190200041.


Duarte, S., L. Nunes, P. Borges, et al. (2018). “A bridge too far? An integrative framework linking classical protist taxonomy and metabarcoding in lower termites”. In: Frontiers in Microbiology 9.NOV. DOI: 10.3389/fmicb.2018.02620.