Missing microbial eukaryotes and misleading meta-omic conclusions

Krinos, Arianna I.; Mars Brisbin, Margaret; Hu, Sarah K.; Cohen, Natalie R.; Rynearson, Tatiana A.; Follows, Michael J.; Schulz, Frederik; Alexander, Harriet

doi:10.1038/s41467-024-52212-w

Missing microbial eukaryotes and misleading meta-omic conclusions

Journal Article · Thu Nov 14 00:00:00 EST 2024 · Nature Communications

DOI:https://doi.org/10.1038/s41467-024-52212-w· OSTI ID:2477448

^[1]; Mars Brisbin, Margaret ^[2]; Hu, Sarah K. ^[3]; ^[4]; ^[5]; ^[6]; ^[7]; ^[8]

Massachusetts Institute of Technology (MIT), Cambridge, MA (United States); Woods Hole Oceanographic Institution, Woods Hole, MA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute
Woods Hole Oceanographic Institution, Woods Hole, MA (United States); University of South Florida, St. Petersburg, FL (United States)
Texas A & M University, College Station, TX (United States)
University of Georgia, Savannah, GA (United States)
University of Rhode Island, Narragansett, RI (United States)
Massachusetts Institute of Technology (MIT), Cambridge, MA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Joint Genome Institute
Woods Hole Oceanographic Institution, Woods Hole, MA (United States)

Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.

View Journal Article

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Simons Foundation; USDOE; USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; SC0020347

OSTI ID:: 2477448

Alternate ID(s):: OSTI ID: 2530313

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 15; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (82)

ggplot2 Wickham, Hadley Springer New York, NY https://doi.org/10.1007/978-0-387-98141-3	book	January 2009
A taxonomic review of the genus Phaeocystis Medlin, Linda; Zingone, Adriana Phaeocystis, major link in the biogeochemical cycling of climate-relevant elements, p. 3-18 https://doi.org/10.1007/978-1-4020-6214-8_2	book	January 2007
The life cycle of Phaeocystis: state of knowledge and presumptive role in ecology Rousseau, Véronique; Chrétiennot-Dinet, Marie-Josèphe; Jacobsen, Anita Biogeochemistry, Vol. 83, Issue 1-3 https://doi.org/10.1007/s10533-007-9085-3	journal	April 2007
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Afshinnekoo, Ebrahim; Meydan, Cem; Chowdhury, Shanin Cell Systems, Vol. 1, Issue 1 https://doi.org/10.1016/j.cels.2015.07.006	journal	July 2015
Marine Protists Are Not Just Big Bacteria Keeling, Patrick J.; Campo, Javier del Current Biology, Vol. 27, Issue 11 https://doi.org/10.1016/j.cub.2017.03.075	journal	June 2017
Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community Semmouri, Ilias; De Schamphelaere, Karel A. C.; Mees, Jan Marine Environmental Research, Vol. 153 https://doi.org/10.1016/j.marenvres.2019.104836	journal	January 2020
Structure-guided metagenome mining to tap microbial functional diversity Robinson, Serina L. Current Opinion in Microbiology, Vol. 76 https://doi.org/10.1016/j.mib.2023.102382	journal	December 2023
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean Delmont, Tom O.; Gaia, Morgan; Hinsinger, Damien D. Cell Genomics, Vol. 2, Issue 5 https://doi.org/10.1016/j.xgen.2022.100123	journal	May 2022
Metagenome assembled genomes are for eukaryotes too Massana, Ramon; López-Escardó, David Cell Genomics, Vol. 2, Issue 5 https://doi.org/10.1016/j.xgen.2022.100130	journal	May 2022
Significance of predation by protists in aquatic microbial food webs Sherr, Evelyn B.; Sherr, Barry F. Antonie van Leeuwenhoek, Vol. 81, Issue 1, p. 293-308 https://doi.org/10.1023/A:1020591307260	journal	March 2002
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic Allen, Lisa Zeigler; Allen, Eric E.; Badger, Jonathan H. The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.201	journal	January 2012
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities Dupont, Chris L.; McCrow, John P.; Valas, Ruben The ISME Journal, Vol. 9, Issue 5 https://doi.org/10.1038/ismej.2014.198	journal	October 2014
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
Full-length transcriptome assembly from RNA-Seq data without a reference genome Grabherr, Manfred G.; Haas, Brian J.; Yassour, Moran Nature Biotechnology, Vol. 29, Issue 7 https://doi.org/10.1038/nbt.1883	journal	May 2011
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Steinegger, Martin; Söding, Johannes Nature Biotechnology, Vol. 35, Issue 11 https://doi.org/10.1038/nbt.3988	journal	October 2017
Probing the evolution, ecology and physiology of marine protists using transcriptomics Caron, David A.; Alexander, Harriet; Allen, Andrew E. Nature Reviews Microbiology, Vol. 15, Issue 1 https://doi.org/10.1038/nrmicro.2016.160	journal	November 2016
Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling Cohen, Natalie R.; Krinos, Arianna I.; Kell, Riss M. Nature Communications, Vol. 15, Issue 1 https://doi.org/10.1038/s41467-024-51583-4	journal	August 2024
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes Delmont, Tom O.; Quince, Christopher; Shaiber, Alon Nature Microbiology, Vol. 3, Issue 7 https://doi.org/10.1038/s41564-018-0176-9	journal	June 2018
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean Royo-Llonch, Marta; Sánchez, Pablo; Ruiz-González, Clara Nature Microbiology, Vol. 6, Issue 12 https://doi.org/10.1038/s41564-021-00979-9	journal	November 2021
Tara Oceans: towards global ocean ecosystems biology Sunagawa, Shinichi; Acinas, Silvia G.; Bork, Peer Nature Reviews Microbiology, Vol. 18, Issue 8 https://doi.org/10.1038/s41579-020-0364-5	journal	May 2020
SciPy 1.0: fundamental algorithms for scientific computing in Python Virtanen, Pauli; Gommers, Ralf; Oliphant, Travis E. Nature Methods https://doi.org/10.1038/s41592-019-0686-2	journal	February 2020
Sensitive protein alignments at tree-of-life scale using DIAMOND Buchfink, Benjamin; Reuter, Klaus; Drost, Hajk-Georg Nature Methods, Vol. 18, Issue 4 https://doi.org/10.1038/s41592-021-01101-x	journal	April 2021
Nanopore sequencing improves the draft genome of the human pathogenic amoeba Naegleria fowleri Liechti, Nicole; Schürch, Nadia; Bruggmann, Rémy Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-52572-0	journal	November 2019
Flexible protein database based on amino acid k-mers Déraspe, Maxime; Boisvert, Sébastien; Laviolette, François Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-12843-9	journal	June 2022
MORPHOLOGICAL AND GENETIC CHARACTERIZATION OF PHAEOCYSTIS CORDATA AND P. JAHNII (PRYMNESIOPHYCEAE), TWO NEW SPECIES FROM THE MEDITERRANEAN SEA Zingone, Adriana; Chrétiennot‐Dinet, Marie‐Josèphe; Lange, Martin Journal of Phycology, Vol. 35, Issue 6 https://doi.org/10.1046/j.1529-8817.1999.3561322.x	journal	December 1999
An original mode of symbiosis in open ocean plankton Decelle, Johan; Probert, Ian; Bittner, Lucie Proceedings of the National Academy of Sciences, Vol. 109, Issue 44 https://doi.org/10.1073/pnas.1212303109	journal	October 2012
Metatranscriptome analyses indicate resource partitioning between diatoms in the field Alexander, Harriet; Jenkins, Bethany D.; Rynearson, Tatiana A. Proceedings of the National Academy of Sciences, Vol. 112, Issue 17 https://doi.org/10.1073/pnas.1421993112	journal	April 2015
Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae Uwizeye, Clarisse; Mars Brisbin, Margaret; Gallet, Benoit Proceedings of the National Academy of Sciences, Vol. 118, Issue 27 https://doi.org/10.1073/pnas.2025252118	journal	July 2021
The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics Lambert, Bennett S.; Groussman, Ryan D.; Schatz, Megan J. Proceedings of the National Academy of Sciences, Vol. 119, Issue 7 https://doi.org/10.1073/pnas.2100916119	journal	February 2022
Tiara: deep learning-based classification system for eukaryotic sequences Karlicki, Michał; Antonowicz, Stanisław; Karnkowska, Anna Bioinformatics, Vol. 38, Issue 2 https://doi.org/10.1093/bioinformatics/btab672	journal	September 2021
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
UniRef: comprehensive and non-redundant UniProt reference clusters Suzek, B. E.; Huang, H.; McGarvey, P. Bioinformatics, Vol. 23, Issue 10 https://doi.org/10.1093/bioinformatics/btm098	journal	March 2007
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses Capella-Gutierrez, S.; Silla-Martinez, J. M.; Gabaldon, T. Bioinformatics, Vol. 25, Issue 15 https://doi.org/10.1093/bioinformatics/btp348	journal	June 2009
NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads Rosen, G. L.; Reichenberger, E. R.; Rosenfeld, A. M. Bioinformatics, Vol. 27, Issue 1 https://doi.org/10.1093/bioinformatics/btq619	journal	November 2010
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes Johnson, Lisa K.; Alexander, Harriet; Brown, C. Titus GigaScience, Vol. 8, Issue 4 https://doi.org/10.1093/gigascience/giy158	journal	December 2018
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data Bushmanova, Elena; Antipov, Dmitry; Lapidus, Alla GigaScience, Vol. 8, Issue 9 https://doi.org/10.1093/gigascience/giz100	journal	September 2019
Genomes OnLine Database (GOLD) v.8: overview and updates Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa983	journal	November 2020
The MAR databases: development and implementation of databases specific for marine metagenomics Klemetsen, Terje; Raknes, Inge A.; Fu, Juan Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1036	journal	November 2017
The Ocean Gene Atlas: exploring the biogeography of plankton genes online Villar, Emilie; Vannier, Thomas; Vernette, Caroline Nucleic Acids Research, Vol. 46, Issue W1 https://doi.org/10.1093/nar/gky376	journal	May 2018
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
How marine currents and environment shape plankton genomic differentiation: a mosaic view from Tara Oceans metagenomic data Laso-Jadart, Romuald; O’Malley, Michael; Sykulski, Adam M. https://doi.org/10.1101/2021.04.29.441957	preprint	April 2021
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Genome-reconstruction for eukaryotes from complex natural microbial communities West, Patrick T.; Probst, Alexander J.; Grigoriev, Igor V. Genome Research, Vol. 28, Issue 4 https://doi.org/10.1101/gr.228429.117	journal	March 2018
Genomic differentiation of three pico‐phytoplankton species in the Mediterranean Sea Da Silva, Ophélie; Ayata, Sakina‐Dorothée; Ser‐Giacomi, Enrico Environmental Microbiology, Vol. 24, Issue 12 https://doi.org/10.1111/1462-2920.16171	journal	August 2022
DNA metabarcoding focused on difficult‐to‐culture protists: An effective approach to clarify biological interactions Nakamura, Yasuhide; Itagaki, Hiryori; Tuji, Akihiro Environmental Microbiology, Vol. 25, Issue 12 https://doi.org/10.1111/1462-2920.16524	journal	October 2023
A metagenomic assessment of microbial eukaryotic diversity in the global ocean Obiol, Aleix; Giner, Caterina R.; Sánchez, Pablo Molecular Ecology Resources, Vol. 20, Issue 3 https://doi.org/10.1111/1755-0998.13147	journal	March 2020
Differential Gene Expression Supports a Resource‐Intensive, Defensive Role for Colony Production in the Bloom‐Forming Haptophyte, Phaeocystis globosa Mars Brisbin, Margaret; Mitarai, Satoshi Journal of Eukaryotic Microbiology, Vol. 66, Issue 5 https://doi.org/10.1111/jeu.12727	journal	March 2019
Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes Worden, A. Z.; Follows, M. J.; Giovannoni, S. J. Science, Vol. 347, Issue 6223 https://doi.org/10.1126/science.1257594	journal	February 2015
Spatiotemporal Variations in Antarctic Protistan Communities Highlight Phytoplankton Diversity and Seasonal Dominance by a Novel Cryptophyte Lineage Hamilton, Maria; Mascioni, Martina; Hehenberger, Elisabeth mBio, Vol. 12, Issue 6 https://doi.org/10.1128/mBio.02973-21	journal	December 2021
mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking Bokulich, Nicholas A.; Rideout, Jai Ram; Mercurio, William G. mSystems, Vol. 1, Issue 5 https://doi.org/10.1128/mSystems.00062-16	journal	October 2016
Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton Alexander, Harriet; Hu, Sarah K.; Krinos, Arianna I. mBio, Vol. 14, Issue 6 https://doi.org/10.1128/mbio.01676-23	journal	December 2023
Efficient string matching: an aid to bibliographic search Aho, Alfred V.; Corasick, Margaret J. Communications of the ACM, Vol. 18, Issue 6 https://doi.org/10.1145/360825.360855	journal	June 1975
Marine Protistan Diversity Caron, David A.; Countway, Peter D.; Jones, Adriane C. Annual Review of Marine Science, Vol. 4, Issue 1 https://doi.org/10.1146/annurev-marine-120709-142802	journal	January 2012
Metagenome Fragment Classification Using -Mer Frequency Profiles Rosen, Gail; Garbarine, Elaine; Caseiro, Diamantino Advances in Bioinformatics, Vol. 2008 https://doi.org/10.1155/2008/205969	journal	January 2008
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Kraken: ultrafast metagenomic sequence classification using exact alignments Wood, Derrick E.; Salzberg, Steven L. Genome Biology, Vol. 15, Issue 3 https://doi.org/10.1186/gb-2014-15-3-r46	journal	January 2014
Decontaminating eukaryotic genome assemblies with machine learning Fierst, Janna L.; Murdock, Duncan A. BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1941-0	journal	December 2017
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly Krinos, Arianna I.; Cohen, Natalie R.; Follows, Michael J. BMC Bioinformatics, Vol. 24, Issue 1 https://doi.org/10.1186/s12859-022-05121-y	journal	March 2023
OrthoFinder: phylogenetic orthology inference for comparative genomics Emms, David M.; Kelly, Steven Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1832-y	journal	November 2019
Improved metagenomic analysis with Kraken 2 Wood, Derrick E.; Lu, Jennifer; Langmead, Ben Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1891-0	journal	November 2019
Mycofier: a new machine learning-based classifier for fungal ITS sequences Delgado-Serrano, Luisa; Restrepo, Silvia; Bustos, Jose Ricardo BMC Research Notes, Vol. 9, Issue 1 https://doi.org/10.1186/s13104-016-2203-3	journal	August 2016
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics Levy Karin, Eli; Mirdita, Milot; Söding, Johannes Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00808-x	journal	April 2020
Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics Cao, Shunan; Zhang, Weipeng; Ding, Wei Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00826-9	journal	April 2020
Evaluating metagenomic assembly approaches for biome-specific gene catalogues Delgado, Luis Fernando; Andersson, Anders F. Microbiome, Vol. 10, Issue 1 https://doi.org/10.1186/s40168-022-01259-2	journal	May 2022
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing Keeling, Patrick J.; Burki, Fabien; Wilcox, Heather M. PLoS Biology, Vol. 12, Issue 6 https://doi.org/10.1371/journal.pbio.1001889	journal	June 2014
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
General Patterns of Diversity in Major Marine Microeukaryote Lineages Pernice, Massimo C.; Logares, Ramiro; Guillou, Laure PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0057170	journal	February 2013
sourmash: a library for MinHash sketching of DNA Titus Brown, C.; Irber, Luiz The Journal of Open Source Software, Vol. 1, Issue 5 https://doi.org/10.21105/joss.00027	journal	September 2016
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes Krinos, Arianna; Hu, Sarah; Cohen, Natalie Journal of Open Source Software, Vol. 6, Issue 57 https://doi.org/10.21105/joss.02817	journal	January 2021
EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes Richter, Daniel J.; Berney, Cédric; Strassert, Jürgen F. H. Peer Community Journal, Vol. 2 https://doi.org/10.24072/pcjournal.173	journal	September 2022
Population genetics: the next stop for microbial ecologists? Logares, Ramiro Open Life Sciences, Vol. 6, Issue 6 https://doi.org/10.2478/s11535-011-0086-9	journal	November 2011
ggmap: Spatial Visualization with ggplot2 Kahle, David; Wickham, Hadley The R Journal, Vol. 5, Issue 1 https://doi.org/10.32614/RJ-2013-014	journal	January 2013
Marine Microeukaryote Metatranscriptomics: Sample Processing and Bioinformatic Workflow Recommendations for Ecological Applications Cohen, Natalie R.; Alexander, Harriet; Krinos, Arianna I. Frontiers in Marine Science, Vol. 9 https://doi.org/10.3389/fmars.2022.867007	journal	June 2022
Diel-Regulated Transcriptional Cascades of Microbial Eukaryotes in the North Pacific Subtropical Gyre Groussman, Ryan D.; Coesel, Sacha N.; Durham, Bryndan P. Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.682651	journal	September 2021
First Draft Genome of the Trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing d’Avila-Levy, Claudia M.; Bearzatto, Bertrand; Ambroise, Jérôme Tropical Medicine and Infectious Disease, Vol. 5, Issue 1 https://doi.org/10.3390/tropicalmed5010025	journal	February 2020
Recent Advances in Application of Transcriptomics: Research on Heterotrophic and Autotrophic Protists Anderson, O. Roger Acta Protozoologica, Vol. 61 https://doi.org/10.4467/16890027AP.22.003.16206	journal	January 2022
EukZoo, an aquatic protistan protein database for meta-omics studies. Liu, Zhenfeng; Hu, Sarah; Caron, David Zenodo https://doi.org/10.5281/zenodo.1476236	dataset	January 2018
Taxonomic annotation errors incorrectly assign the family Pseudoalteromonadaceae to the order Vibrionales in Greengenes: implications for microbial community assessments Lydon, Keri Ann; Lipp, Erin K. PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5248	journal	January 2018
Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria Hernández, Laura; Vicens, Alberto; Eguiarte, Luis E. PeerJ, Vol. 8 https://doi.org/10.7717/peerj.9861	journal	September 2020

Similar Records

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

Journal Article · Thu Jun 19 00:00:00 EDT 2014 · Frontiers in Microbiology · OSTI ID:1392592

Improvement of eukaryotic protein predictions from soil metagenomes

Journal Article · Wed Jun 15 20:00:00 EDT 2022 · Scientific Data · OSTI ID:1904105

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Missing microbial eukaryotes and misleading meta-omic conclusions

Citation Formats

References (82)

Similar Records

Related Subjects