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The Earth Microbiome project: successes and aspirations
Open accessAbstract
The Earth Microbiome Project (EMP) was launched in August 2010, with the ambitious aim of constructing a global catalogue of the uncultured microbial diversity of this planet.The primary vision of the Earth Microbiome Project, to process the microbial diversity and functional potential from approximately 200,000 environmental samples, marks it as an undertaking so massive that it was at first considered to be pure folly (as late as 2012, Jonathan Eisen was quoted in Nature as saying 'Knight and Gilbert literally talk about sampling the entire planet.It is ludicrous and not feasible -yet they are doing it' [1]).The initial concept arose out of a Department of the Environment (DOE) sponsored workshop on the promise of terabase-scale sequencing in Snowbird, Utah, de-
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Cites
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
Self-citationStructure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems
Zinger, L., Amaral-Zettler, L. A., Fuhrman, J. A., Horner-Devine, M. C., Huse, S. M., Welch, D. B. M., Martiny, J. B. H., Sogin, M., Boetius, A., & Ramette, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024570 · Cited by 643 · cited 1×
“International Census of Marine Microbes [5] and the Human Microbiome Project [6].”
Background
Research works printed but not linked: 18
- Gewin V: Microbes en masse: The sequencing machine. Nature. 2012, 487: 156-158. 10.1038/487156a. · DOI
- Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, Desai N, Eisen JA, Evers D, Field D, Feng W, Huson D, Jansson J, Knight R, Knight J, Kolker E, Konstantindis K, Kostka J, Kyrpides N, Mackelprang R, McHardy A, Quince C, Raes J, Sczyrba A, Shade A, Stevens R: Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genomic Sci. 2010, 3: 243-248. 10.4056/sigs.1433550. · DOI · Paper page
- Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner F-O, Klenk H-P, Wommack KE, Glass E, Docherty K, Gallery R, Stevens R, Knight R: The Earth Microbiome Project: Meeting report of the “1 EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Stand Genomic Sci. 2010, 3: 249-253. 10.4056/aigs.1443528. · DOI · Paper page
- NIH Human Microbiome Project (HMP) Roadmap Project.., [http://www.ncbi.nlm.nih.gov/bioproject/43021]
- Piombino P, Genovese A, Esposito S, Moio L, Cutolo PP, Chambery A, Severino V, Moneta E, Smith DP, Owens SM, Gilbert JA, Ercolini D: Saliva from obese individuals suppresses the release of aroma compounds from wine. PLoS One. 2014, 9: e85611-10.1371/journal.pone.0085611. · DOI
- Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL: Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013, 342: 621-624. 10.1126/science.1243768. · DOI · Paper page
- Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Capek P, Santrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik VL, Schleper C, Urich T: Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J. 2014, 8: 841-853. 10.1038/ismej.2013.219. · DOI
- Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK: Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 2014, 8: 1464-1475. 10.1038/ismej.2013.254. · DOI · Paper page
- Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA: The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Front Microbiol. 2014, 5: 108-10.3389/fmicb.2014.00108. · DOI
- Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA: Human and environmental impacts on river sediment microbial communities. PLoS One. 2014, 9: e97435-10.1371/journal.pone.0097435. · DOI
- McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P: An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012, 6: 610-618. 10.1038/ismej.2011.139. · DOI · Paper page
- Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R, Gilbert JA: Evidence for a persistent microbial seed bank throughout the global ocean. Proc Natl Acad Sci U S A. 2013, 110: 4651-4655. 10.1073/pnas.1217767110. · DOI · Paper page
- Rubin BER, Gibbons SM, Kennedy S, Hampton-Marcell J, Owens S, Gilbert JA: Investigating the impact of storage conditions on microbial community composition in soil samples. PLoS ONE. 2013, 8: e70460-10.1371/journal.pone.0070460. · DOI
- Zehr JP, Crumbliss LL, Church MJ, Omoregie EO, Jenkins BD: Nitrogenase genes in PCR and RT-PCR reagents: implications for studies of diversity of functional genes. BioTechniques. 2003, 35: 996-1002. 1004–1005 · doi:10.2144/03355st08
- Gilbert JA, Bailey M, Field D, Fierer N, Fuhrman JA, Hu B, Jansson J, Knight R, Kowalchuk GA, Kyrpides NC, Meyer F, Stevens R: The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011. Stand Genomic Sci. 2011, 5: 243-247. 10.4056/sigs.2134923. · doi:10.4056/sigs.2134923
- McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG: The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience. 2012, 1: 7-10.1186/2047-217X-1-7. · DOI · Paper page
- Chen VB, Davis IW, Richardson DC: KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. Protein Sci Publ Protein Soc. 2009, 18: 2403-2409. 10.1002/pro.250. · DOI
- Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R: EMPeror: a tool for visualizing high-throughput microbial community data. GigaScience. 2013, 2: 16-10.1186/2047-217X-2-16. · DOI · Paper page
Cited by
VSEARCH: a versatile open source tool for metagenomics
(2016) · doi:10.7717/peerj.2584 · Cited by 10,773
Gut microbiota regulate motor deficits and neuroinflammation in a model of Parkinson's disease
Sampson, T. R., Debelius, J. W., Thron, T., Janssen, S., Shastri, G. G., Ilhan, Z. E., Challis, C., Schretter, C. E., Rocha, S., Gradinaru, V., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.018 · Cited by 3,622
Self-citationA communal catalogue reveals Earth's multiscale microbial diversity
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., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684
Self-citationApprill, A., McNally, S., Parsons, R., & Weber, L. (2015) · Aquatic Microbial Ecology · doi:10.3354/ame01753 · Cited by 2,707
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624
Self-citation
Metadata
- Authors
- Gilbert, J. A., Jansson, J. K., & Knight, R.
- Venue
- BMC Biology
- Published
- 2014-08-22
- Volume
- 12
- Issue
- 1
- Pages
- 69-69
- ISSN
- 1741-7007 (ISSN-L)
- OpenAlex
- W2106399600
- Cited by
- 878
- References
- 3
- FWCI
- 57.90
- Type
- journal article
- Language
- en
- Open access
- gold
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