A communal catalogue reveals Earth's multiscale microbial diversity
Open accessAbstract
Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
At present, all 96 individual studies that make up the Earth Microbiome Project are grouped together under a single Super Study, as are MGnify analyses for 8 distinct Tara Oceans datasets.
“For example, at present, all 96 individual studies that make up the Earth Microbiome Project (18) are grouped together under a single Super Study, as are MGnify analyses for 8 distinct Tara Oceans (19) datasets.”
From MGnify: the microbiome analysis resource in 2020 (2019) · cites this paper as [18]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
A Mathematical Theory of Communication
Shannon, C. E. (1948) · Bell System Technical Journal · doi:10.1002/j.1538-7305.1948.tb01338.x · Cited by 88,486 · see citing works
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
Self-citationThe SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099 · see citing works
Self-citationClassification and Regression by randomForest
Liaw, A. I., & Wiener, M. C. (2007) · Cited by 18,594 · see citing works
VSEARCH: a versatile open source tool for metagenomics
(2016) · doi:10.7717/peerj.2584 · Cited by 10,773 · see citing works
Building Predictive Models in R Using the caret Package
Kühn, M. (2008) · Journal of Statistical Software · doi:10.18637/jss.v028.i05 · Cited by 9,986 · see citing works
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,633 · see citing works
Self-citationPredictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works
Self-citationUltra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839 · see citing works
Self-citationThe diversity and biogeography of soil bacterial communities
Fierer, N., & Jackson, R. B. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507535103 · Cited by 5,711 · see citing works
Self-citationConservation evaluation and phylogenetic diversity
Faith, D. (1992) · Biological Conservation · doi:10.1016/0006-3207(92)91201-3 · Cited by 5,495 · see citing works
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works
Self-citationRibosomal Database Project: data and tools for high throughput rRNA analysis
Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras‐Alfaro, A., Kuske, C. R., & Tiedje, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1244 · Cited by 4,322 · see citing works
Nonparametric estimation of the number of classes in a population
Chao, A. (1984) · Scandinavian Journal of Statistics · Cited by 4,263 · see citing works
Parada, A. E., Needham, D. M., & Fuhrman, J. A. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13023 · Cited by 4,026 · see citing works
Self-citationGoing back to the roots: the microbial ecology of the rhizosphere
Philippot, L., Raaijmakers, J. M., Lemanceau, P., & van der Putten, W. H. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3109 · Cited by 3,925 · see citing works
Microbial diversity in the deep sea and the underexplored “rare biosphere”
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. B. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605127103 · Cited by 3,683 · see citing works
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463 · see citing works
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
Callahan, B. J., McMurdie, P. J., & Holmes, S. (2017) · The ISME Journal · doi:10.1038/ismej.2017.119 · Cited by 3,253 · see citing works
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
Kopylova, E., Noé, L., & Touzet, H. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts611 · Cited by 3,051 · see citing works
Self-citationApprill, A., McNally, S., Parsons, R., & Weber, L. (2015) · Aquatic Microbial Ecology · doi:10.3354/ame01753 · Cited by 2,707 · see citing works
Self-citationWalters, W. A., Hyde, E. R., Berg-Lyons, D., Ackermann, G. L., Humphrey, G. C., Parada, A. E., Gilbert, J. A., Jansson, J. K., Caporaso, J. G., Fuhrman, J. A., et al. (2015) · mSystems · doi:10.1128/msystems.00009-15 · Cited by 2,202 · see citing works
Self-citationReducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112 · see citing works
On the Generality of the Latitudinal Diversity Gradient
Hillebrand, H. (2004) · The American Naturalist · doi:10.1086/381004 · Cited by 2,067 · see citing works
A new view of the tree of life
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.48 · Cited by 2,039 · see citing works
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
Amir, A., McDonald, D., Navas-Molina, J. A., Kopylova, E., Morton, J. T., Zech Xu, Z., Kightley, E. P., Thompson, L. R., Hyde, E. R., Gonzalez, A., et al. (2017) · mSystems · doi:10.1128/msystems.00191-16 · Cited by 1,881 · see citing works
Self-citationBayesian community-wide culture-independent microbial source tracking
Knights, D., Kuczynski, J., Charlson, E. S., Zaneveld, J., Mozer, M. C., Collman, R. G., Bushman, F. D., Knight, R. D., & Kelley, S. T. (2011) · Nature Methods · doi:10.1038/nmeth.1650 · Cited by 1,839 · see citing works
Self-citationGlobal patterns in bacterial diversity
Lozupone, C., & Knight, R. D. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611525104 · Cited by 1,832 · see citing works
Self-citationAlmeida‐Neto, M., Guimarães, P. R., Guimarães, P. R., Loyola, R. A., & Ulrich, W. (2008) · Oikos · doi:10.1111/j.0030-1299.2008.16644.x · Cited by 1,741 · see citing works
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
Worlds within worlds: evolution of the vertebrate gut microbiota
Ley, R. E., Lozupone, C., Hamady, M., Knight, R. D., & Gordon, J. I. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1978 · Cited by 1,652 · see citing works
Self-citationPattern and Process in Macroecology
Gaston, K. J., & Blackburn, T. M. (2000) · Wiley eBooks · doi:10.1002/9780470999592 · Cited by 1,572 · see citing works
The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta‐analyses
IOANNIDIS, J. P. A. (2016) · The Milbank Quarterly · doi:10.1111/1468-0009.12210 · Cited by 1,483 · see citing works
Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss
Dornelas, M., Gotelli, N. J., McGill, B., Shimadzu, H., Moyes, F., Sievers, C., & Magurran, A. E. (2014) · Science · doi:10.1126/science.1248484 · Cited by 1,412 · see citing works
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346 · see citing works
A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
Eddy, S. R. (2009) · International Conference on Genome Informatics (GIW) · doi:10.1142/9781848165632_0019 · Cited by 1,275 · see citing works
EMPeror: a tool for visualizing high-throughput microbial community data
Vázquez‐Baeza, Y., Pirrung, M., Gonzalez, A., & Knight, R. D. (2013) · GigaScience · doi:10.1186/2047-217x-2-16 · Cited by 1,272 · see citing works
Self-citationCython: The Best of Both Worlds
Behnel, S., Bradshaw, R., Citro, C., Dalcín, L., Seljebotn, D. S., & Smith, K. (2010) · Computing in Science & Engineering · doi:10.1109/mcse.2010.118 · Cited by 1,233 · see citing works
rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
Klappenbach, J. A., Dunbar, J., & Schmidt, T. M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.4.1328-1333.2000 · Cited by 1,140 · see citing works
Hamady, M., Lozupone, C., & Knight, R. D. (2009) · The ISME Journal · doi:10.1038/ismej.2009.97 · Cited by 1,100 · see citing works
Self-citationMicrobial Ecology and Evolution: A Ribosomal RNA Approach
Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., & Stahl, D. A. (1986) · Annual Review of Microbiology · doi:10.1146/annurev.mi.40.100186.002005 · Cited by 1,078 · see citing works
The measure of order and disorder in the distribution of species in fragmented habitat
Atmar, W., & Patterson, B. D. (1993) · Oecologia · doi:10.1007/bf00317508 · Cited by 1,028 · see citing works
Matsen, F. A., IV, Kodner, R. B., & Armbrust, E. V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-538 · Cited by 1,026 · see citing works
Determinants of community structure in the global plankton interactome
Lima‐Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio‐Espinoza, J. C., Roux, S., Vincent, F., et al. (2015) · Science · doi:10.1126/science.1262073 · Cited by 967 · see citing works
Self-citationMcDonald, D. T., Clemente, J. C., Kuczynski, J., Rideout, J. R., Stombaugh, J., Wendel, D., Wilke, A., Huse, S. M., Hufnagle, J., Meyer, F., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-7 · Cited by 901 · see citing works
Self-citationThe Earth Microbiome project: successes and aspirations
Gilbert, J. A., Jansson, J. K., & Knight, R. D. (2014) · BMC Biology · doi:10.1186/s12915-014-0069-1 · Cited by 879 · see citing works
Self-citationA consumer's guide to nestedness analysis
Ulrich, W., Almeida‐Neto, M., & Gotelli, N. J. (2008) · Oikos · doi:10.1111/j.1600-0706.2008.17053.x · Cited by 830 · see citing works
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, D. M., Vangay, P., Garbe, J., Maclean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R. C., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3601 · Cited by 807 · see citing works
Self-citationYilmaz, P., Kottmann, R., Field, D., Knight, R. D., Cole, J. R., Amaral‐Zettler, L., Gilbert, J. A., Karsch‐Mizrachi, I., Johnston, A., Cochrane, G., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1823 · Cited by 802 · see citing works
Self-citationA latitudinal diversity gradient in planktonic marine bacteria
Fuhrman, J. A., Steele, J. A., Hewson, I., Schwalbach, M. S., Brown, M. V., Green, J. L., & Brown, J. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803070105 · Cited by 733 · see citing works
Self-citationUberon, an integrative multi-species anatomy ontology
Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., & Haendel, M. A. (2012) · Genome biology · doi:10.1186/gb-2012-13-1-r5 · Cited by 732 · see citing works
Temperature mediates continental-scale diversity of microbes in forest soils
Zhou, J. Z., Deng, Y., Shen, L., Wen, C., Yan, Q., Ning, D., Qin, Y., Xue, K., Wu, L., He, Z., et al. (2016) · Nature Communications · doi:10.1038/ncomms12083 · Cited by 693 · see citing works
Self-citationOrmerod, K. L., Wood, D., Lachner, N., Gellatly, S. L., Daly, J. N., Parsons, J. D., Dal’Molin, C. G. D. O., Palfreyman, R. W., Nielsen, L. K., Cooper, M. A., et al. (2016) · Microbiome · doi:10.1186/s40168-016-0181-2 · Cited by 675 · see citing works
Marine bacterial, archaeal and protistan association networks reveal ecological linkages
Steele, J. A., Countway, P. D., Xia, L., Vigil, P. D., Beman, J. M., Kim, D. Y., Chow, C.-E. T., Sachdeva, R., Jones, A. C., Schwalbach, M. S., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.24 · Cited by 634 · see citing works
Self-citationChu, H., Fierer, N., Lauber, C. L., Caporaso, J. G., Knight, R. D., & Grogan, P. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02277.x · Cited by 606 · see citing works
Self-citationRideout, J. R., He, Y., Navas-Molina, J. A., Walters, W. A., Ursell, L. K., Gibbons, S. M., Chase, J., McDonald, D. T., Gonzalez, A., Robbins‐Pianka, A., et al. (2014) · PeerJ · doi:10.7717/peerj.545 · Cited by 550 · see citing works
Self-citationA meta-analysis of changes in bacterial and archaeal communities with time
Shade, A. L., Caporaso, J. G., Handelsman, J., Knight, R. D., & Fierer, N. (2013) · The ISME Journal · doi:10.1038/ismej.2013.54 · Cited by 399 · see citing works
Self-citationThe environment ontology: contextualising biological and biomedical entities
Buttigieg, P. L., Morrison, N., Smith, B., Mungall, C., & Lewis, S. (2013) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-4-43 · Cited by 359 · see citing works
Spatial Gaps in Global Biodiversity Information and the Role of Citizen Science
Amano, T., Lamming, J. D. L., & Sutherland, W. J. (2016) · BioScience · doi:10.1093/biosci/biw022 · Cited by 286 · see citing works
Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Brown, C. T., Desai, N., Eisen, J. A., Evers, D., Field, D., et al. (2010) · Standards in Genomic Sciences · doi:10.4056/sigs.1433550 · Cited by 274 · see citing works
Self-citationButtigieg, P. L., Pafilis, E., Lewis, S., Schildhauer, M. P., Walls, R., & Mungall, C. (2016) · Journal of Biomedical Semantics · doi:10.1186/s13326-016-0097-6 · Cited by 270 · see citing works
Investigating causality of nestedness of insular communities: selective immigrations or extinctions?
Lomolino, M. V. (1996) · Journal of Biogeography · doi:10.1111/j.1365-2699.1996.tb00030.x · Cited by 260 · see citing works
SEPP: SATé-Enabled Phylogenetic Placement
MIRARAB, S., NGUYEN, N., & WARNOW, T. (2011) · Biocomputing 2012 · doi:10.1142/9789814366496_0024 · Cited by 251 · see citing works
Self-citationGlobal marine bacterial diversity peaks at high latitudes in winter
Ladau, J., Sharpton, T. J., Finucane, M. M., Jospin, G., Kembel, S. W., O’Dwyer, J. P., Koeppel, A. F., Green, J. L., & Pollard, K. S. (2013) · The ISME Journal · doi:10.1038/ismej.2013.37 · Cited by 219 · see citing works
Self-citationA unified initiative to harness Earth's microbiomes
Alivisatos, A. P., Blaser, M. J., Brodie, E., Chun, M., Dangl, J. L., Donohue, T. J., Dorrestein, P. C., Gilbert, J. A., Green, J. L., Jansson, J. K., et al. (2015) · Science · doi:10.1126/science.aac8480 · Cited by 218 · see citing works
Self-citationCarvalho, J. C., Cardoso, P., Borges, P. A. V., et al. (2012) · Oikos · doi:10.1111/j.1600-0706.2012.20980.x · Cited by 216 · see citing works
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
Eloe-Fadrosh, E., Ivanova, N., Woyke, T., & Kyrpides, N. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2015.32 · Cited by 216 · see citing works
Decreases in average bacterial community rRNA operon copy number during succession
Nemergut, D. R., Knelman, J. E., Ferrenberg, S. M., Bilinski, T. M., Melbourne, B. A., Jiang, L., Violle, C., Darcy, J. L., Prest, T. L., Schmidt, S. K., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.191 · Cited by 213 · see citing works
Self-citationWu, Y., Zeng, J., Zhu, Q., Zhang, Z., & Lin, X. (2017) · Scientific Reports · doi:10.1038/srep40093 · Cited by 199 · see citing works
Self-citationThe Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
Cooper, L., Walls, R., Elser, J. L., Gandolfo, M. A., Stevenson, D. W., Smith, B., Preece, J., Athreya, B., Mungall, C., Rensing, S. A., et al. (2012) · Plant and Cell Physiology · doi:10.1093/pcp/pcs163 · Cited by 175 · see citing works
Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem
Gibbons, S. M., Lekberg, Y., Mummey, D. L., Sangwan, N., Ramsey, P. W., & Gilbert, J. A. (2017) · mSystems · doi:10.1128/msystems.00178-16 · Cited by 161 · see citing works
Self-citationConsistently inconsistent drivers of microbial diversity and abundance at macroecological scales
Hendershot, J. N., Read, Q. D., Henning, J. A., Sanders, N. J., & Classen, A. T. (2017) · Ecology · doi:10.1002/ecy.1829 · Cited by 153 · see citing works
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Goodwin, K. D., Thompson, L., Duarte, B., Kahlke, T., Thompson, A. R., Marques, J. C., & Caçador, I. (2017) · Frontiers in Marine Science · doi:10.3389/fmars.2017.00107 · Cited by 124 · see citing works
Self-citationPasteurella multocida—The major cause of hand infections following domestic animal bites
Arons, M. S., Fernando, L., & Polayes, I. M. (1982) · The Journal Of Hand Surgery · doi:10.1016/s0363-5023(82)80013-0 · Cited by 81 · see citing works
Low diversity of planktonic bacteria in the tropical ocean
Milici, M., Tomasch, J., Wos‐Oxley, M. L., et al. (2016) · Scientific Reports · doi:10.1038/srep19054 · Cited by 81 · see citing works
Guo, W., Sarkar, S. K., & Peddada, S. D. (2009) · Biometrics · doi:10.1111/j.1541-0420.2009.01292.x · Cited by 55 · see citing works
The founding charter of the Genomic Observatories Network
GOs-COS, Davies, N., Field, D., et al. (2014) · GigaScience · doi:10.1186/2047-217x-3-2 · Cited by 47 · see citing works
An ontology for microbial phenotypes
Chibucos, M. C., Zweifel, A. E., Herrera, J. C., Meza, W., Eslamfam, S., Uetz, P., Siegele, D. A., Hu, J. C., & Giglio, M. G. (2014) · BMC Microbiology · doi:10.1186/s12866-014-0294-3 · Cited by 41 · see citing works
Quantifying human impact on Earth's microbiome
Pointing, S. B., Fierer, N., Smith, G. J. D., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.145 · Cited by 21 · see citing works
Self-citationGrandhi, A., Guo, W., & Peddada, S. D. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-0937-5 · Cited by 15 · see citing works
Simple and efficient fully-functional succinct trees
Cordova, J., & Navarro, G. (2016) · Theoretical Computer Science · doi:10.1016/j.tcs.2016.04.031 · Cited by 10 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143 · see citing works
Self-citationDeciphering cell–cell interactions and communication from gene expression
Armingol, E., Officer, A., Harismendy, O., & Lewis, N. E. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00292-x · Cited by 1,267 · see citing works
American Gut: an Open Platform for Citizen-Science Microbiome Research
McDonalda, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., Aksenov, A. A., Behsaz, B., Brennan, C., Chen, Y., et al. (2018) · doi:10.1101/277970 · Cited by 878 · see citing works
Self-citationCurrent challenges and best-practice protocols for microbiome analysis
Bharti, R., & Grimm, D. G. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbz155 · Cited by 592 · see citing works
MGnify: the microbiome analysis resource in 2020
Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562 · see citing works
Evaluating the Information Content of Shallow Shotgun Metagenomics
Hillmann, B., Al-Ghalith, G. A., Shields-Cutler, R. R., Zhu, Q., Gohl, D. M., Beckman, K. B., Knight, R., & Knights, D. (2018) · mSystems · doi:10.1128/msystems.00069-18 · Cited by 474 · see citing works
Self-citationMills, R. H., Dulai, P. S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R. R., Batachari, L. E., Malfavon, M., Zhu, Q., Weldon, K., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-021-01050-3 · Cited by 385 · see citing works
Self-citationRoslund, M. I., Puhakka, R., Grönroos, M., Nurminen, N., Oikarinen, S., Gazali, A. M., Cinek, O., Kramná, L., Siter, N., Vari, H. K., et al. (2020) · Science Advances · doi:10.1126/sciadv.aba2578 · Cited by 363 · see citing works
Fructose stimulated de novo lipogenesis is promoted by inflammation
Todoric, J., Di Caro, G., Reibe, S., Henstridge, D. C., Green, C. R., Vrbanac, A., Ceteci, F., Conche, C., McNulty, R., Shalapour, S., et al. (2020) · Nature Metabolism · doi:10.1038/s42255-020-0261-2 · Cited by 328 · see citing works
Self-citationPérez-Cobas, A. E., Gomez-Valero, L., & Buchrieser, C. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000409 · Cited by 314 · see citing works
Bacterial Candidates for Colonization and Degradation of Marine Plastic Debris
Roager, L., & Sonnenschein, E. C. (2019) · Environmental Science & Technology · doi:10.1021/acs.est.9b02212 · Cited by 305 · see citing works
High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Zheng, W., Zhao, S., Yin, Y., Zhang, H., Needham, D. M., Evans, E. D., Dai, C. L., Lu, P. J., Alm, E. J., & Weitz, D. A. (2022) · Science · doi:10.1126/science.abm1483 · Cited by 283 · see citing works
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works
Self-citationMicrobiota succession throughout life from the cradle to the grave
Martino, C., Dilmore, A. H., Burcham, Z. M., Metcalf, J. L., Jeste, D., & Knight, R. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00768-z · Cited by 275 · see citing works
Self-citationDynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring
Jiang, C., Wang, X., Li, X., Inlora, J., Wang, T., Liu, Q., & Snyder, M. (2018) · Cell · doi:10.1016/j.cell.2018.08.060 · Cited by 218 · see citing works
Self-citationRocca, J. D., Simonin, M., Blaszczak, J. R., Ernakovich, J. G., Gibbons, S. M., Midani, F. S., & Washburne, A. D. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03272 · Cited by 213 · see citing works
Self-citationPatterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study
Burcham, Z. M., Garneau, N. L., Comstock, S. S., Tucker, R. M., Knight, R., Metcalf, J. L., Scientists, G. O. T. L. C., Miranda, A., Reinhart, B., Meyers, D., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-59016-0 · Cited by 183 · see citing works
Self-citationZabat, M. A., Sano, W. H., Wurster, J. I., Cabral, D. J., & Belenky, P. (2018) · Foods · doi:10.3390/foods7050077 · Cited by 160 · see citing works
The best practice for microbiome analysis using R
Wen, T., Niu, G., Chen, T., Shen, Q., Yuan, J., & Liu, Y.-X. (2023) · Protein & Cell · doi:10.1093/procel/pwad024 · Cited by 139 · see citing works
Self-citationChen, Y.-R., Zheng, H.-M., Zhang, G.-X., Chen, F.-L., Chen, L.-D., & Yang, Z.-C. (2020) · Scientific Reports · doi:10.1038/s41598-020-66369-z · Cited by 127 · see citing works
Peters, B. A., Lin, J., Qi, Q., Usyk, M., Isasi, C. R., Mossavar-Rahmani, Y., Derby, C. A., Santoro, N., Perreira, K. M., Daviglus, M. L., et al. (2022) · mSystems · doi:10.1128/msystems.00273-22 · Cited by 130 · see citing works
Self-citationThe need for an integrated multi-OMICs approach in microbiome science in the food system
Ferrocino, I., Rantsiou, K., McClure, R., Kostic, T., de Souza, R. S. C., Lange, L., FitzGerald, J., Kriaa, A., Cotter, P., Maguin, E., et al. (2023) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.13103 · Cited by 110 · see citing works
Ighalo, J. O., Ohoro, C. R., Ojukwu, V. E., Oniye, M., Shaikh, W. A., Biswas, J. K., Seth, C. S., Mohan, G. B. M., Chandran, S. A., & Rangabhashiyam, S. (2025) · iScience · doi:10.1016/j.isci.2024.111524 · Cited by 107 · see citing works
Maricic, I., Marrero, I., Eguchi, A., Nakamura, R., Johnson, C. D., Dasgupta, S., Hernandez, C. D., Nguyen, P. S., Swafford, A. D., Knight, R., et al. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1800614 · Cited by 92 · see citing works
Self-citationThe confluence of big data and evolutionary genome mining for the discovery of natural products
Chevrette, M. G., Gavrilidou, A., Mantri, S., Selem-Mojica, N., Ziemert, N., & Barona-Gómez, F. (2021) · Natural Product Reports · doi:10.1039/d1np00013f · Cited by 66 · see citing works
Functional Strain Redundancy and Persistent Phage Infection in Swiss Hard Cheese Starter Cultures
Somerville, V., Berthoud, H., Schmidt, R. S., Bachmann, H.-P., Meng, Y. H., Fuchsmann, P., von Ah, U., & Engel, P. (2022) · The ISME Journal · doi:10.1038/s41396-021-01071-0 · Cited by 55 · see citing works
Gut microbiome strain-sharing within isolated village social networks
Beghini, F., Pullman, J., Alexander, M., Shridhar, S. V., Prinster, D., Singh, A., Matute Juárez, R., Airoldi, E. M., Brito, I. L., & Christakis, N. A. (2025) · Nature · doi:10.1038/s41586-024-08222-1 · Cited by 51 · see citing works
Zhou, Z., Li, Z., Chen, K., Chen, Z., Zeng, X., Yu, H., Guo, S., Shangguan, Y., Chen, Q., Fan, H., et al. (2021) · SOIL · doi:10.5194/soil-7-595-2021 · Cited by 39 · see citing works
Microbiome and -omics application in food industry
Ferrocino, I., Rantsiou, K., & Cocolin, L. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.109781 · Cited by 34 · see citing works
Jin, J., Yamamoto, R., & Shiroguchi, K. (2024) · Nature Protocols · doi:10.1038/s41596-023-00906-8 · Cited by 33 · see citing works
The role of microbiota in allogeneic hematopoietic stem cell transplantation
Chang, C.-C., Hayase, E., & Jenq, R. R. (2021) · Expert Opinion on Biological Therapy · doi:10.1080/14712598.2021.1872541 · Cited by 20 · see citing works
Universal Drivers of Cheese Microbiomes
Reuben, R. C., Langer, D., Eisenhauer, N., & Jurburg, S. D. (2023) · iScience · doi:10.1016/j.isci.2022.105744 · Cited by 21 · see citing works
Self-citationGhaly, T. M., Rajabal, V., Russell, D., Colombi, E., & Tetu, S. G. (2025) · doi:10.1101/2025.04.02.646905 · Cited by 5 · see citing works
Biegert, G., Karpinets, T., Wu, X., Alam, M. B. E., Sims, T. T., Yoshida-Court, K., Lynn, E. J., Yue, J., Medrano, A. D., Petrosino, J., et al. (2020) · doi:10.1101/2020.05.05.080002 · Cited by 1 · see citing works
- Authors
- Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M. F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich, N. A., Lefler, J., Brislawn, C. J., Humphrey, G., Owens, S. M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J. A., Clauset, A., Stevens, R. L., Shade, A., Pollard, K. S., Goodwin, K. D., Jansson, J. K., Gilbert, J. A., Knight, R., The Earth Microbiome Project Consortium, Rivera, J. L. A., Al-Moosawi, L., Alverdy, J., Amato, K. R., Andras, J., Angenent, L. T., Antonopoulos, D. A., Apprill, A., Armitage, D., Ballantine, K., Bárta, J., Baum, J. K., Berry, A., Bhatnagar, A., Bhatnagar, M., Biddle, J. F., Bittner, L., Boldgiv, B., Bottos, E., Boyer, D. M., Braun, J., Brazelton, W., Brearley, F. Q., Campbell, A. H., Caporaso, J. G., Cardona, C., Carroll, J., Cary, S. C., Casper, B. B., Charles, T. C., Chu, H., Claar, D. C., Clark, R. G., Clayton, J. B., Clemente, J. C., Cochran, A., Coleman, M. L., Collins, G., Colwell, R. R., Contreras, M., Crary, B. B., Creer, S., Cristol, D. A., Crump, B. C., Cui, D., Daly, S. E., Davalos, L., Dawson, R. D., Defazio, J., Delsuc, F., Dionisi, H. M., Dominguez-Bello, M. G., Dowell, R., Dubinsky, E. A., Dunn, P. O., Ercolini, D., Espinoza, R. E., Ezenwa, V., Fenner, N., Findlay, H. S., Fleming, I. D., Fogliano, V., Forsman, A., Freeman, C., Friedman, E. S., Galindo, G., Garcia, L., Garcia-Amado, M. A., Garshelis, D., Gasser, R. B., Gerdts, G., Gibson, M. K., Gifford, I., Gill, R. T., Giray, T., Gittel, A., Golyshin, P., Gong, D., Grossart, H.-P., Guyton, K., Haig, S.-J., Hale, V., Hall, R. S., Hallam, S. J., Handley, K. M., Hasan, N. A., Haydon, S. R., Hickman, J. E., Hidalgo, G., Hofmockel, K. S., Hooker, J., Hulth, S., Hultman, J., Hyde, E., Ibáñez-Álamo, J. D., Jastrow, J. D., Jex, A. R., Johnson, L. S., Johnston, E. R., Joseph, S., Jurburg, S. D., Jurelevicius, D., Karlsson, A., Karlsson, R., Kauppinen, S., Kellogg, C. T. E., Kennedy, S. J., Kerkhof, L. J., King, G. M., Kling, G. W., Koehler, A. V., Krezalek, M., Kueneman, J., Lamendella, R., Landon, E. M., Lane-deGraaf, K., LaRoche, J., Larsen, P., Laverock, B., Lax, S., Lentino, M., Levin, I. I., Liancourt, P., Liang, W., Linz, A. M., Lipson, D. A., Liu, Y., Lladser, M. E., Lozada, M., Spirito, C. M., MacCormack, W. P., MacRae-Crerar, A., Magris, M., Martín-Platero, A. M., Martín-Vivaldi, M., Martínez, L. M., Martínez-Bueno, M., Marzinelli, E. M., Mason, O. U., Mayer, G. D., McDevitt-Irwin, J. M., McDonald, J. E., McGuire, K. L., McMahon, K. D., McMinds, R., Medina, M., Mendelson, J. R., Metcalf, J. L., Meyer, F., Michelangeli, F., Miller, K., Mills, D. A., Minich, J., Mocali, S., Moitinho-Silva, L., Moore, A., Morgan-Kiss, R. M., Munroe, P., Myrold, D., Neufeld, J. D., Ni, Y., Nicol, G. W., Nielsen, S., Nissimov, J. I., Niu, K., Nolan, M. J., Noyce, K., O’Brien, S. L., Okamoto, N., Orlando, L., Castellano, Y. O., Osuolale, O., Oswald, W., Parnell, J., Peralta-Sánchez, J. M., Petraitis, P., Pfister, C., Pilon-Smits, E., Piombino, P., Pointing, S. B., Pollock, F. J., Potter, C., Prithiviraj, B., Quince, C., Rani, A., Ranjan, R., Rao, S., Rees, A. P., Richardson, M., Riebesell, U., Robinson, C., Rockne, K. J., Rodriguezl, S. M., Rohwer, F., Roundstone, W., Safran, R. J., Sangwan, N., Sanz, V., Schrenk, M., Schrenzel, M. D., Scott, N. M., Seger, R. L., Seguin-Orlando, A., Seldin, L., Seyler, L. M., Shakhsheer, B., Sheets, G. M., Shen, C., Shi, Y., Shin, H., Shogan, B. D., Shutler, D., Siegel, J., Simmons, S., Sjöling, S., Smith, D. P., Soler, J. J., Sperling, M., Steinberg, P. D., Stephens, B., Stevens, M. A., Taghavi, S., Tai, V., Tait, K., Tan, C. L., Tas¸, N., Taylor, D. L., Thomas, T., Timling, I., Turner, B. L., Urich, T., Ursell, L. K., van der Lelie, D., Van Treuren, W., van Zwieten, L., Vargas-Robles, D., Thurber, R. V., Vitaglione, P., Walker, D. A., Walters, W. A., Wang, S., Wang, T., Weaver, T., Webster, N. S., Wehrle, B., Weisenhorn, P., Weiss, S., Werner, J. J., West, K., Whitehead, A., Whitehead, S. R., Whittingham, L. A., Willerslev, E., Williams, A. E., Wood, S. A., Woodhams, D. C., Yang, Y., Zaneveld, J., Zarraonaindia, I., Zhang, Q., & Zhao, H.
- Affiliations
- National Oceanic and Atmospheric Administration (US)
- University of California San Diego (US)
- Gladstone Institutes (US)
- Indiana University Bloomington (US)
- IBM Research - Almaden (US)
- Broad Institute (US)
- Harvard University (US)
- Northern Arizona University (US)
- Pacific Northwest National Laboratory (US)
- Argonne National Laboratory (US)
- University of Colorado Boulder (US)
- Cooperative Institute for Research in Environmental Sciences (US)
- University of Southern California (US)
- Michigan State University (US)
- Plymouth Marine Laboratory (GB)
- University of Chicago (US)
- Northwestern University (US)
- Mount Holyoke College (US)
- Cornell University (US)
- Woods Hole Oceanographic Institution (US)
- University of Notre Dame (US)
- University of Victoria (CA)
- University of California, Davis (US)
- Maharshi Dayanand Saraswati University (IN)
- University of Delaware (US)
- Évolution Paris Seine (FR)
- National University of Mongolia (MN)
- Wildlife Conservation Society (US)
- San Diego Zoo Institute for Conservation Research (US)
- University of Utah (US)
- Manchester Metropolitan University (GB)
- UNSW Sydney (AU)
- UiT The Arctic University of Norway (NO)
- University of Waikato (NZ)
- University of Pennsylvania (US)
- University of Waterloo (CA)
- Chinese Academy of Sciences (CN)
- Environment and Climate Change Canada (CA)
- University of Minnesota (US)
- Colorado State University (US)
- Ollscoil na Gaillimhe – University of Galway (IE)
- University of Maryland, College Park (US)
- Instituto Venezolano de Investigaciones Científicas (VE)
- University of Wisconsin–Madison (US)
- Bangor University (GB)
- William & Mary (US)
- Oregon State University (US)
- Purdue University West Lafayette (US)
- University of Northern British Columbia (CA)
- Centre National de la Recherche Scientifique (FR)
- Centro Científico Tecnológico Patagónico (AR)
- University of California, Berkeley (US)
- University of Wisconsin–Milwaukee (US)
- University of Naples Federico II (IT)
- California State University, Northridge (US)
- University of Georgia (US)
- Vanderbilt University (US)
- Lawrence Berkeley National Laboratory (US)
- University of Puerto Rico System (PR)
- Minnesota Department of Natural Resources (US)
- The University of Melbourne (AU)
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung (DE)
- Washington University in St. Louis (US)
- Aarhus University (DK)
- Virginia Institute of Marine Science (US)
- University of Potsdam (DE)
- University of Michigan (US)
- The Ohio State University (US)
- University of British Columbia (CA)
- University of Auckland (NZ)
- Melbourne Water (AU)
- Columbia University (US)
- Chief Dull Knife College (US)
- University of Gothenburg (SE)
- University of Helsinki (FI)
- Towson University (US)
- Georgia Institute of Technology (US)
- Wageningen University & Research (NL)
- Universidade Federal do Rio de Janeiro (BR)
- Biomatics, Inc. (Japan) (JP)
- Rutgers, The State University of New Jersey (US)
- Louisiana State University (US)
- Juniata College (US)
- Fontbonne University (US)
- Dalhousie University (CA)
- University of Technology Sydney (AU)
- Colección Ornitológica Phelps (VE)
- University of Tübingen (DE)
- San Diego State University (US)
- Universidad de Granada (ES)
- Florida State University (US)
- Texas Tech University (US)
- University of Oregon (US)
- Pennsylvania State University (US)
- Morningside College (US)
- Université de Lyon (FR)
- Fanjingshan National Nature Reserve (CN)
- Université Toulouse III - Paul Sabatier (FR)
- Elizade University (NG)
- Emerson College (US)
- Novozymes (United States) (US)
- Auckland University of Technology (NZ)
- City University of New York (US)
- University of Warwick (GB)
- University of Illinois Chicago (US)
- GEOMAR Helmholtz Centre for Ocean Research Kiel (DE)
- University of East Anglia (GB)
- University of Maine (US)
- Emory University (US)
- Sejong University (KR)
- University of Toronto (CA)
- Södertörn University (SE)
- Baylor College of Medicine (US)
- Consejo Superior de Investigaciones Científicas (ES)
- Illinois Institute of Technology (US)
- Western University (CA)
- University of New Mexico (US)
- University of Alaska Fairbanks (US)
- Smithsonian Tropical Research Institute (PA)
- University of Vienna (AT)
- Max Planck Institute for Developmental Biology (DE)
- Australian Institute of Marine Science (AU)
- University of California, Irvine (US)
- SUNY Cortland (US)
- Virginia Tech (US)
- University of Copenhagen (DK)
- Yale University (US)
- University of Massachusetts Boston (US)
- Tongren University (CN)
- University of Washington Bothell (US)
- University of the Basque Country (ES)
- Corresponding author
- Knight, Rob
- ORCID
- Thompson, Luke R.
- Sanders, Jon G.
- McDonald, Daniel
- Amir, Amnon
- Ladau, Joshua
- Locey, Kenneth J.
- Tripathi, Anupriya
- Gibbons, Sean M.
- Ackermann, Gail
- Navas-Molina, Jose A.
- Kopylova, Evguenia
- González, Antonio
- Morton, James T.
- Mirarab, Siavash
- Jiang, Lingjing
- Haroon, Mohamed F.
- Kanbar, Jad
- Zhu, Qiyun
- Bokulich, Nicholas A.
- Brislawn, Colin J.
- Humphrey, Gregory
- Owens, Sarah M.
- McKenzie, Valerie
- Fierer, Noah
- Fuhrman, Jed A.
- Clauset, Aaron
- Stevens, Rick L.
- Shade, Ashley
- Pollard, Katherine S.
- Goodwin, Kelly D.
- Jansson, Janet K.
- Gilbert, Jack A.
- Knight, Rob
- Alverdy, John
- Amato, Katherine R.
- Andras, Jason
- Angenent, Largus T.
- Antonopoulos, Dionysios A.
- Apprill, Amy
- Ballantine, Kate
- Baum, Julia K.
- Bhatnagar, Ashish
- Biddle, Jennifer F.
- Bittner, Lucie
- Boldgiv, Bazartseren
- Bottos, Eric
- Brazelton, William
- Brearley, Francis Q.
- Campbell, Alexandra H.
- Caporaso, J. Gregory
- Carroll, JoLynn
- Cary, S. Craig
- Charles, Trevor C.
- Chu, Haiyan
- Claar, Danielle C.
- Clark, Robert G.
- Clayton, Jonathan B.
- Coleman, Maureen L.
- Collins, Gavin
- Colwell, Rita R.
- Contreras, Mónica
- Crary, Benjamin B.
- Creer, Simon
- Cristol, Daniel A.
- Crump, Byron C.
- Dawson, Russell D.
- Defazio, Jennifer
- Delsuc, Frédéric
- Dionisi, Hebe M.
- Dowell, Robin
- Dubinsky, Eric A.
- Dunn, Peter O.
- Ercolini, Danilo
- Espinoza, Robert E.
- Ezenwa, Vanessa
- Fenner, Nathalie
- Findlay, Helen S.
- Fleming, Irma D.
- Fogliano, Vincenzo
- Forsman, Anna
- Freeman, Chris
- Friedman, Elliot S.
- Garshelis, David
- Gasser, Robin B.
- Gerdts, Gunnar
- Gibson, Molly K.
- Gifford, Isaac
- Gill, Ryan T.
- Gittel, Antje
- Golyshin, Peter
- Gong, Donglai
- Grossart, Hans-Peter
- Guyton, Kristina
- Haig, Sarah-Jane
- Hale, Vanessa
- Hall, Ross Stephen
- Hallam, Steven J.
- Handley, Kim M.
- Hasan, Nur A.
- Haydon, Shane R.
- Hickman, Jonathan E.
- Hofmockel, Kirsten S.
- Hulth, Stefan
- Hultman, Jenni
- Jastrow, Julie D.
- Jex, Aaron R.
- Johnson, L. Scott
- Johnston, Eric R.
- Jurburg, Stephanie D.
- Jurelevicius, Diogo
- Karlsson, Anders
- Karlsson, Roger
- Kauppinen, Seth
- Kellogg, Colleen T. E.
- Kerkhof, Lee J.
- King, Gary M.
- Kling, George W.
- Koehler, Anson V.
- Krezalek, Monika
- Kueneman, Jordan
- Lamendella, Regina
- Landon, Emily M.
- LaRoche, Julie
- Laverock, Bonnie
- Lax, Simon
- Lentino, Miguel
- Levin, Iris I.
- Liancourt, Pierre
- Linz, Alexandra M.
- Lipson, David A.
- Liu, Yongqin
- Lladser, Manuel E.
- Lozada, Mariana
- Martín-Platero, Antonio M.
- Marzinelli, Ezequiel M.
- Mason, Olivia U.
- Mayer, Gregory D.
- McDonald, James E.
- McGuire, Krista L.
- McMahon, Katherine D.
- McMinds, Ryan
- Medina, Mónica
- Mendelson, Joseph R.
- Metcalf, Jessica L.
- Meyer, Folker
- Mills, David A.
- Minich, Jeremiah
- Munroe, Paul
- Myrold, David
- Neufeld, Josh D.
- Ni, Yingying
- Nicol, Graeme W.
- Nissimov, Jozef I.
- Niu, Kefeng
- Nolan, Matthew J.
- Noyce, Karen
- Okamoto, Noriko
- Orlando, Ludovic
- Osuolale, Olayinka
- Parnell, Jacob
- Petraitis, Peter
- Pfister, Catherine
- Piombino, Paola
- Pointing, Stephen B.
- Pollock, F. Joseph
- Potter, Caitlin
- Prithiviraj, Bharath
- Quince, Christopher
- Rani, Asha
- Ranjan, Ravi
- Rao, Subramanya
- Rees, Andrew P.
- Richardson, Miles
- Riebesell, Ulf
- Robinson, Carol
- Rockne, Karl J.
- Rohwer, Forest
- Safran, Rebecca J.
- Sangwan, Naseer
- Schrenk, Matthew
- Scott, Nicole M.
- Seldin, Lucy
- Seyler, Lauren M.
- Shakhsheer, Baddr
- Shen, Congcong
- Shi, Yu
- Shin, Hakdong
- Shogan, Benjamin D.
- Siegel, Jeffrey
- Sjöling, Sara
- Smith, Daniel P.
- Soler, Juan J.
- Steinberg, Peter D.
- Stephens, Brent
- Stevens, Melita A.
- Tai, Vera
- Tait, Karen
- Tan, Chia L.
- Taylor, D. Lee
- Thomas, Torsten
- Timling, Ina
- Turner, Benjamin L.
- Urich, Tim
- Vargas-Robles, Daniela
- Vitaglione, Paola
- Walker, Donald A.
- Walters, William A.
- Wang, Tao
- Webster, Nicole S.
- Wehrle, Beck
- Weisenhorn, Pamela
- Werner, Jeffrey J.
- Whitehead, Andrew
- Whitehead, Susan R.
- Whittingham, Linda A.
- Willerslev, Eske
- Wood, Stephen A.
- Woodhams, Douglas C.
- Zaneveld, Jesse
- Zarraonaindia, Iratxe
- Venue
- Nature
- Published
- 2017-11-01
- Volume
- 551
- Issue
- 7681
- Pages
- 457-463
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6192678
- OpenAlex
- W2766358903
- Cited by
- 2,684
- References
- 83
- Citations by year
- 2026: 255 · 2025: 326 · 2024: 304 · 2023: 329 · 2022: 334 · 2021: 405 · 2020: 321 · 2019: 259 · 2018: 143 · 2017: 4 · 2016: 2
- FWCI
- 149.56
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, cc-by)
- Helmholtz Centre for Ocean Research Kiel (GEOMAR) (acceptedVersion, other-oa)
- Marine Biological Association (acceptedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (acceptedVersion, cc-by)
- UEA Digital Repository (University of East Anglia) (acceptedVersion)
- Warwick Research Archive Portal (University of Warwick) (acceptedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- e-space (Manchester Metropolitan University) (acceptedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- Aquila Digital Community (University of Southern Mississippi) (submittedVersion, cc-by)
- Civil War Book Review (submittedVersion, cc-by)
- Työväentutkimus Vuosikirja (submittedVersion, cc-by)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- Civil War Book Review (submittedVersion)
- W&M Publish (College of William & Mary) (submittedVersion)
- Journal of International Crisis and Risk Communication Research (submittedVersion)
- UNSWorks (UNSW Sydney) (submittedVersion, cc-by-nc-nd)
- HAL (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Americanae (AECID Library) (submittedVersion, cc-by-nc-sa)
- ASEP (submittedVersion, public-domain)
- Tuwhera (Auckland University of Technology) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, cc-by)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- NOAA Institutional Repository (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- PUB – Publications at Bielefeld University (Bielefeld University) (submittedVersion)
- Publikationen an der Universität Bielefeld (Universität Bielefeld) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Griffith Research Online (submittedVersion, cc-by)
- Bangor University Research Portal (Bangor University) (submittedVersion, other-oa)
- UNSWorks (University of New South Wales, Sydney, Australia) (submittedVersion, cc-by-nc-nd)
- VTechWorks (Virginia Tech) (submittedVersion, cc-by)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- ETH Zürich Research Collection (cc-by)
- Funders
- National Science Foundation (DE-AC02–06CH11357, 1053575, BIO150043)
- U.S. Department of Energy (DE‐ AC02‐06CH11357, ACI-1053575, AC02‐06CH11357, contract DE-AC02-06CH11357, 06CH11357, DE-AC02-)
- W. M. Keck Foundation (DT061413)
- John Templeton Foundation (44000)
- Mississippi State University
- Northern Gulf Institute
- Lawrence Foundation
- Tula Foundation
- Lundbeckfonden (R109-2012-9995, R70-2010-6286, R155-2013-16338, R38-2008-3048, R24-2008-2527)
- National Oceanic and Atmospheric Administration
- Natural Environment Research Council (pml010009, pml010007, NE/K00168X/1)
- Australian Research Council
- National Institute of Allergy and Infectious Diseases (R01AI123037)
- National Institute of Dental and Craniofacial Research (R01DE024463)
- Argonne National Laboratory (DE- AC02-06-CH11357, DE-AC02, AC02–06CH11357, 06CH11357)
- NOAA's Atlantic Oceanographic and Meteorological Laboratory
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- microbial diversity, Earth Microbiome Project, reference database, ribosomal RNA gene sequences, bacterial diversity, archaeal diversity, operational taxonomic units, standardized protocols
- MeSH terms
- Animals, Archaea, Bacteria, Ecology, Humans, Plants, RNA, Ribosomal, 16S, Earth, Planet, Gene Dosage, Biodiversity, Geographic Mapping, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
