Publications

Publications deriving from individual EMP studies

Over 60 papers have been published using sequence data generated by the Earth Microbiome Project. A partial list of those publications is provided below. Just for fun, we calculated the impact factor of these publications, totaling 62 as of September 2017. These papers had on average 17 citations per paper per year. Code for this calculation is available on GitHub.

Publications using EMP protocols

Based on citations of two publications describing the EMP protocols, nearly 2000 publications have used the EMP protocols in their methods. See the Google Scholar statistics: Caporaso et al., PNAS, 2011; Caporaso et al., ISME Journal, 2012.

Publications using EMP for meta-analysis

The primary EMP meta-analysis was published in Nature on 1 November 2017: Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., …, Jansson, J. K., Gilbert, J. A., Knight, R., and The Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551:457-463. doi:10.1038/nature24621.

The first analysis of the EMP multi-omics dataset was published in Nature Microbiology on 28 November 2022: Shaffer, J.P.*, L.-F. Nothias*, L.R. Thompson*, J.G. Sanders, R.A. Salido, S.P. Couvillion, A.D. Brejnrod, S. Huang, F. Lejzerowicz, H.L. Lutz, Q. Zhu, C. Martino, J.T. Morton, S. Karthikeyan, M. Nothias-Esposito, K. Dürkhop, S. Böcker, H. Kim, A.A. Aksenov, W. Bittremieux, J.J. Minich, C. Marotz, M.M. Bryant, K. Sanders, G. Humphrey, Y. Vasquez-Baeza, A. Tripathi, L. Parida, A.P. Carrieri, N. Haiminen, K.L. Beck, P. Das, A. Gonzalez, D. McDonald, J. Ladau, S.M. Karst, M. Albertsen, G. Ackermann, J. DeReus, T. Thomas, D. Petras, J. Stegen, S.J. Song, T.O. Metz, A.D. Swafford, P.C. Dorrestein, J. Jansson, J.A. Gilbert, R. Knight, and the Earth Microbiome Project 500 Consortium. (2022). Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature Microbiology 7:2128-2150. *These authors contributed equally. doi: 10.1038/s41564-022-01266-x.

Testing of macroecological theories applied to microbial communities has produced insights into ecological scaling laws and species abundance distributions. Read the papers: Locey et al., PNAS, 2016; Shoemaker et al., Nat Ecol Evol, 2017.

Software development

Deblur, a recently published method for resolving exact, error-free sequences from amplicon sequencing data, has been deployed in the EMP meta-analysis to great effect, permitting the tracking of microbial taxa across Earth’s microbial communities. Read the paper: Amir et al., mSystems, 2017.
Many additional software tools, including QIIME, UniFrac, and EMPeror, have undergone significant improvements to allow them to scale to the tens of thousands of samples in this meta-analysis. These improvements have benefitted many other projects and contributed to their success. The EMP has also driven methods development of many other computational techniques, e.g., co-abundance and differential abundance.

List of publications deriving from EMP data

  • Armitage, D. W. (2016). Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community. doi:10.1101/090225
  • Bartram, A. K., Jiang, X., Lynch, M. D. J., Masella, A. P., Nicol, G. W., Dushoff, J., & Neufeld, J. D. (2013). Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS Microbiology Ecology, 87(2), 403–415. doi:10.1111/1574-6941.12231
  • Bielewicz, S., Bell, E., Kong, W., Friedberg, I., Priscu, J. C., & Morgan-Kiss, R. M. (2011). Protist diversity in a permanently ice-covered Antarctic Lake during the polar night transition. The ISME Journal, 5(9), 1559–1564. doi:10.1038/ismej.2011.23
  • Brazelton, W. J., Nelson, B., & Schrenk, M. O. (2012). Metagenomic Evidence for H2 Oxidation and H2 Production by Serpentinite-Hosted Subsurface Microbial Communities. Frontiers in Microbiology, 2. doi:10.3389/fmicb.2011.00268
  • Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., … Knight, R. (2011). Moving pictures of the human microbiome. Genome Biology, 12(5), R50. doi:10.1186/gb-2011-12-5-r50
  • Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., … Knight, R. (2012). Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal, 6(8), 1621–1624. doi:10.1038/ismej.2012.8
  • Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., … Knight, R. (2010). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, 108(Supplement_1), 4516–4522. doi:10.1073/pnas.1000080107
  • Crump, B. C., Amaral-Zettler, L. A., & Kling, G. W. (2012). Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils. The ISME Journal, 6(9), 1629–1639. doi:10.1038/ismej.2012.9
  • Delsuc, F., Metcalf, J. L., Wegener Parfrey, L., Song, S. J., González, A., & Knight, R. (2013). Convergence of gut microbiomes in myrmecophagous mammals. Molecular Ecology, 23(6), 1301–1317. doi:10.1111/mec.12501
  • Espínola, F., Dionisi, H. M., Borglin, S., Brislawn, C. J., Jansson, J. K., Mac Cormack, W. P., … Lozada, M. (2017). Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microbial Ecology. doi:10.1007/s00248-017-1028-5
  • Fierer, N., Ladau, J., Clemente, J. C., Leff, J. W., Owens, S. M., Pollard, K. S., … McCulley, R. L. (2013). Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States. Science, 342(6158), 621–624. doi:10.1126/science.1243768
  • Friedman, E., Miller, K., Lipson, D., & Angenent, L. (2013). Potentiostatically Poised Electrodes Mimic Iron Oxide and Interact with Soil Microbial Communities to Alter the Biogeochemistry of Arctic Peat Soils. Minerals, 3(3), 318–336. doi:10.3390/min3030318
  • Gewin, V. (2012). Microbes en masse: The sequencing machine. Nature, 487(7406), 156–158. doi:10.1038/487156a
  • Gibbons, S. M., Jones, E., Bearquiver, A., Blackwolf, F., Roundstone, W., Scott, N., … Gilbert, J. A. (2014). Human and Environmental Impacts on River Sediment Microbial Communities. PLoS ONE, 9(5), e97435. doi:10.1371/journal.pone.0097435
  • Gilbert, J. A., & Meyer, F. (2012). Modeling the Earth Microbiome. Microbe Magazine, 7(2), 64–69. doi:10.1128/microbe.7.64.1
  • Gilbert, J. A., Jansson, J. K., & Knight, R. (2014). The Earth Microbiome project: successes and aspirations. BMC Biology, 12(1). doi:10.1186/s12915-014-0069-1
  • Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Brown, C. T., … Stevens, R. (2010). Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3(3), 243–248. doi:10.4056/sigs.1433550
  • Gilbert, J. A., Meyer, F., Field, D., Schriml, L. M., & Garrity, G. M. (2010). Metagenomics: A foundling finds its feet. Standards in Genomic Sciences, 3(2), 212–213. doi:10.4056/sigs.1213842
  • Gilbert, J. A., Meyer, F., Jansson, J., Gordon, J., Pace, N., Tiedje, J., … Knight, R. (2010). The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010. Standards in Genomic Sciences, 3(3), 249–253. doi:10.4056/aigs.1443528
  • Gilbert, J. A., O’Dor, R., King, N., & Vogel, T. M. (2011). The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist. Microbial Informatics and Experimentation, 1(1), 5. doi:10.1186/2042-5783-1-5
  • Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbrück, L., Reeder, J., Temperton, B., … Field, D. (2011). Defining seasonal marine microbial community dynamics. The ISME Journal, 6(2), 298–308. doi:10.1038/ismej.2011.107
  • Gittel, A., Bárta, J., Kohoutová, I., Mikutta, R., Owens, S., Gilbert, J., … Urich, T. (2013). Distinct microbial communities associated with buried soils in the Siberian tundra. The ISME Journal, 8(4), 841–853. doi:10.1038/ismej.2013.219
  • Glass, E., Meyer, F., Gilbert, J. A., Field, D., Hunter, S., Kottmann, R., … Wooley, J. (2010). Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10. Standards in Genomic Sciences, 3(3), 225–231. doi:10.4056/sigs.1423520
  • Gregg, A., Hatay, M., Haas, A., Robinett, N., Barott, K., Vermeij, M., … Rohwer, F. (2013). Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates. PeerJ, 1, e107. doi:10.7717/peerj.107
  • Haig, S.-J., Quince, C., Davies, R. L., Dorea, C. C., & Collins, G. (2014). Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters. Water Research, 61, 141–151. doi:10.1016/j.watres.2014.05.008
  • Hale, V. L., Tan, C. L., Knight, R., & Amato, K. R. (2015). Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8weeks. Journal of Microbiological Methods, 113, 16–26. doi:10.1016/j.mimet.2015.03.021
  • Hale, V. L., Tan, C. L., Niu, K., Yang, Y., Cui, D., Zhao, H., … Amato, K. R. (2016). Effects of field conditions on fecal microbiota. Journal of Microbiological Methods, 130, 180–188. doi:10.1016/j.mimet.2016.09.017
  • Hyde, E. R., Navas-Molina, J. A., Song, S. J., Kueneman, J. G., Ackermann, G., Cardona, C., … Knight, R. (2016). The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems, 1(4), e00046–16. doi:10.1128/msystems.00046-16
  • Jansson, J. (2011). Towards “Tera-Terra”: Terabase Sequencing of Terrestrial Metagenomes. Microbe Magazine, 6(7), 309–315. doi:10.1128/microbe.6.309.1
  • Jansson, J. K., & Prosser, J. I. (2013). Microbiology: The life beneath our feet. Nature, 494(7435), 40–41. doi:10.1038/494040a
  • Kao, R. H., Gibson, C. M., Gallery, R. E., Meier, C. L., Barnett, D. T., Docherty, K. M., … Schimel, D. (2012). NEON terrestrial field observations: designing continental-scale, standardized sampling. Ecosphere, 3(12), art115. doi:10.1890/es12-00196.1
  • Kara, E. L., Hanson, P. C., Hu, Y. H., Winslow, L., & McMahon, K. D. (2012). A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota, WI, USA. The ISME Journal, 7(3), 680–684. doi:10.1038/ismej.2012.118
  • Karsenti, E., Acinas, S. G., Bork, P., Bowler, C., De Vargas, C., … Raes, J. (2011). A Holistic Approach to Marine Eco-Systems Biology. PLoS Biology, 9(10), e1001177. doi:10.1371/journal.pbio.1001177
  • Knight, R., Jansson, J., Field, D., Fierer, N., Desai, N., Fuhrman, J. A., … Gilbert, J. A. (2012). Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology, 30(6), 513–520. doi:10.1038/nbt.2235
  • Koehler, A. V., Haydon, S. R., Jex, A. R., & Gasser, R. B. (2016). Cryptosporidium and Giardia taxa in faecal samples from animals in catchments supplying the city of Melbourne with drinking water (2011 to 2015). Parasites & Vectors, 9(1). doi:10.1186/s13071-016-1607-1
  • Larsen, P. E., Field, D., & Gilbert, J. A. (2012). Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods, 9(6), 621–625. doi:10.1038/nmeth.1975
  • Laverock, B., Smith, C. J., Tait, K., Osborn, A. M., Widdicombe, S., & Gilbert, J. A. (2010). Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments. The ISME Journal, 4(12), 1531–1544. doi:10.1038/ismej.2010.86
  • Lax, S., Smith, D. P., Hampton-Marcell, J., Owens, S. M., Handley, K. M., Scott, N. M., … Gilbert, J. A. (2014). Longitudinal analysis of microbial interaction between humans and the indoor environment. Science, 345(6200), 1048–1052. doi:10.1126/science.1254529
  • Levin, I. I., Zonana, D. M., Fosdick, B. K., Song, S. J., Knight, R., & Safran, R. J. (2016). Stress response, gut microbial diversity and sexual signals correlate with social interactions. Biology Letters, 12(6), 20160352. doi:10.1098/rsbl.2016.0352
  • Lipson, D. A., Raab, T. K., Parker, M., Kelley, S. T., Brislawn, C. J., & Jansson, J. (2015). Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils. Environmental Microbiology Reports, 7(4), 649–657. doi:10.1111/1758-2229.12301
  • Locey, K. J., & Lennon, J. T. (2016). Scaling laws predict global microbial diversity. Proceedings of the National Academy of Sciences, 113(21), 5970–5975. doi:10.1073/pnas.1521291113
  • Magalhñes, C. M., Machado, A., Frank-Fahle, B., Lee, C. K., & Cary, S. C. (2014). The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00515
  • Marzinelli, E. M., Campbell, A. H., Zozaya Valdes, E., Vergés, A., Nielsen, S., Wernberg, T., … Steinberg, P. D. (2015). Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography. Environmental Microbiology, 17(10), 4078–4088. doi:10.1111/1462-2920.12972
  • Mason, O. U., Scott, N. M., Gonzalez, A., Robbins-Pianka, A., Bælum, J., Kimbrel, J., … Jansson, J. K. (2014). Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. The ISME Journal, 8(7), 1464–1475. doi:10.1038/ismej.2013.254
  • Monier, A., Findlay, H. S., Charvet, S., & Lovejoy, C. (2014). Late winter under ice pelagic microbial communities in the high Arctic Ocean and the impact of short-term exposure to elevated CO2levels. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00490
  • Navas-Molina, J. A., Peralta-Sánchez, J. M., González, A., McMurdie, P. J., Vázquez-Baeza, Y., Xu, Z., … Knight, R. (2013). Advancing Our Understanding of the Human Microbiome Using QIIME. Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, 371–444. doi:10.1016/b978-0-12-407863-5.00019-8
  • Neufeld, J. D., Engel, K., Cheng, J., Moreno-Hagelsieb, G., Rose, D. R., & Charles, T. C. (2011). Open resource metagenomics: a model for sharing metagenomic libraries. Standards in Genomic Sciences, 5(2), 203–210. doi:10.4056/sigs.1974654
  • Nolan, M. J., Jex, A. R., Koehler, A. V., Haydon, S. R., Stevens, M. A., & Gasser, R. B. (2013). Molecular-based investigation of Cryptosporidium and Giardia from animals in water catchments in southeastern Australia. Water Research, 47(5), 1726–1740. doi:10.1016/j.watres.2012.12.027
  • Piombino, P., Genovese, A., Esposito, S., Moio, L., Cutolo, P. P., Chambery, A., … Ercolini, D. (2014). Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine. PLoS ONE, 9(1), e85611. doi:10.1371/journal.pone.0085611
  • Potter, C., Freeman, C., Golyshin, P. N., Ackermann, G., Fenner, N., McDonald, J. E., … Creer, S. (2017). Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems. Scientific Reports, 7(1). doi:10.1038/s41598-017-11546-w
  • Reese, A. T., Savage, A., Youngsteadt, E., McGuire, K. L., Koling, A., Watkins, O., … Dunn, R. R. (2015). Urban stress is associated with variation in microbial species composition—but not richness—in Manhattan. The ISME Journal, 10(3), 751–760. doi:10.1038/ismej.2015.152
  • Roy, A.-S., Gibbons, S. M., Schunck, H., Owens, S., Caporaso, J. G., Sperling, M., … Gilbert, J. A. (2013). Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms. Biogeosciences, 10(1), 555–566. doi:10.5194/bg-10-555-2013
  • Rubin, B. E. R., Gibbons, S. M., Kennedy, S., Hampton-Marcell, J., Owens, S., & Gilbert, J. A. (2013). Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples. PLoS ONE, 8(7), e70460. doi:10.1371/journal.pone.0070460
  • Russell, J. A., Brady, A. L., Cardman, Z., Slater, G. F., Lim, D. S. S., & Biddle, J. F. (2014). Prokaryote populations of extant microbialites along a depth gradient in Pavilion Lake, British Columbia, Canada. Geobiology, 12(3), 250–264. doi:10.1111/gbi.12082
  • Scott, N. M., Hess, M., Bouskill, N. J., Mason, O. U., Jansson, J. K., & Gilbert, J. A. (2014). The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00108
  • Shen, C., Xiong, J., Zhang, H., Feng, Y., Lin, X., Li, X., … Chu, H. (2013). Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biology and Biochemistry, 57, 204–211. doi:10.1016/j.soilbio.2012.07.013
  • Shoemaker, W. R., Locey, K. J., & Lennon, J. T. (2017). A macroecological theory of microbial biodiversity. Nature Ecology & Evolution, 1(5), 0107. doi:10.1038/s41559-017-0107
  • Sura-de Jong, M., Reynolds, R. J. B., Richterova, K., Musilova, L., Staicu, L. C., Chocholata, I., … Pilon-Smits, E. A. H. (2015). Selenium hyperaccumulators harbor a diverse endophytic bacterial community characterized by high selenium resistance and plant growth promoting properties. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00113
  • Taş, N., Prestat, E., McFarland, J. W., Wickland, K. P., Knight, R., Berhe, A. A., … Jansson, J. K. (2014). Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest. The ISME Journal, 8(9), 1904–1919. doi:10.1038/ismej.2014.36
  • Thomas, T., Moitinho-Silva, L., Lurgi, M., Björk, J. R., Easson, C., Astudillo-García, C., … Webster, N. S. (2016). Diversity, structure and convergent evolution of the global sponge microbiome. Nature Communications, 7, 11870. doi:10.1038/ncomms11870
  • Vitaglione, P., Mennella, I., Ferracane, R., Rivellese, A. A., Giacco, R., Ercolini, D., … Fogliano, V. (2014). Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: role of polyphenols bound to cereal dietary fiber. American Journal of Clinical Nutrition, 101(2), 251–261. doi:10.3945/ajcn.114.088120
  • Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., … Cochrane, G. (2011). Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29(5), 415–420. doi:10.1038/nbt.1823
  • Zarraonaindia, I., Owens, S. M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., … Gilbert, J. A. (2015). The Soil Microbiome Influences Grapevine-Associated Microbiota. mBio, 6(2), e02527–14. doi:10.1128/mbio.02527-14

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