A genomic catalog of Earth’s microbiomes

Nayfach, S.; Roux, S.; Seshadri, R.; Udwary, D.; Varghese, N.; Schulz, F.; Wu, D.; Paez-Espino, D.; Chen, I. M.; Huntemann, M.; Palaniappan, K.; Ladau, J.; Mukherjee, S.; Reddy, T. B. K.; Nielsen, T.; Kirton, E.; Faria, J. P.; Edirisinghe, J. N.; Henry, C. S.; Jungbluth, S. P.; Chivian, D.; Dehal, P.; Wood-Charlson, E. M.; Arkin, A. P.; Tringe, S. G.; Visel, A.; Abreu, H.; Acinas, S. G.; Allen, E.; Allen, M. A.; Alteio, L. V.; Andersen, G.; Anesio, A. M.; Attwood, G.; Avila-Magaña, V.; Badis, Y.; Bailey, J.; Baker, B.; Baldrian, P.; Barton, H. A.; Beck, D. A. C.; Becraft, E. D.; Beller, H. R.; Beman, J. M.; Bernier-Latmani, R.; Berry, T. D.; Bertagnolli, A.; Bertilsson, S.; Bhatnagar, J. M.; Bird, J. T.; Blanchard, J. L.; Blumer-Schuette, S. E.; Bohannan, B.; Borton, M. A.; Brady, A.; Brawley, S. H.; Brodie, J.; Brown, S.; Brum, J. R.; Brune, A.; Bryant, D. A.; Buchan, A.; Buckley, D. H.; Buongiorno, J.; Cadillo-Quiroz, H.; Caffrey, S. M.; Campbell, A. N.; Campbell, B.; Carr, S.; Carroll, J. L.; Cary, S. C.; Cates, A. M.; Cattolico, R. A.; Cavicchioli, R.; Chistoserdova, L.; Coleman, M. L.; Constant, P.; Conway, J. M.; Mac Cormack, W. P.; Crowe, S.; Crump, B.; Currie, C.; Daly, R.; DeAngelis, K. M.; Denef, V.; Denman, S. E.; Desta, A.; Dionisi, H.; Dodsworth, J.; Dombrowski, N.; Donohue, T.; Dopson, M.; Driscoll, T.; Dunfield, P.; Dupont, C. L.; Dynarski, K. A.; Edgcomb, V.; Edwards, E. A.; Elshahed, M. S.; Figueroa, I.; Flood, B.; Fortney, N.; Fortunato, C. S.; Francis, C.; Gachon, C. M. M.; Garcia, S. L.; Gazitua, M. C.; Gentry, T.; Gerwick, L.; Gharechahi, J.; Girguis, P.; Gladden, J.; Gradoville, M.; Grasby, S. E.; Gravuer, K.; Grettenberger, C. L.; Gruninger, R. J.; Guo, J.; Habteselassie, M. Y.; Hallam, S. J.; Hatzenpichler, R.; Hausmann, B.; Hazen, T. C.; Hedlund, B.; Henny, C.; Herfort, L.; Hernandez, M.; Hershey, O. S.; Hess, M.; Hollister, E. B.; Hug, L. A.; Hunt, D.; Jansson, J.; Jarett, J.; Kadnikov, V. V.; Kelly, C.; Kelly, R.; Kelly, W.; Kerfeld, C. A.; Kimbrel, J.; Klassen, J. L.; Konstantinidis, K. T.; Lee, L. L.; Li, W. J.; Loder, A. J.; Loy, A.; Lozada, M.; MacGregor, B.; Magnabosco, C.; Maria da Silva, A.; McKay, R. M.; McMahon, K.; McSweeney, C. S.; Medina, M.; Meredith, L.; Mizzi, J.; Mock, T.; Momper, L.; Moran, M. A.; Morgan-Lang, C.; Moser, D.; Muyzer, G.; Myrold, D.; Nash, M.; Nesbø, C. L.; Neumann, A. P.; Neumann, R. B.; Noguera, D.; Northen, T.; Norton, J.; Nowinski, B.; Nüsslein, K.; O’Malley, M. A.; Oliveira, R. S.; Maia de Oliveira, V.; Onstott, T.; Osvatic, J.; Ouyang, Y.; Pachiadaki, M.; Parnell, J.; Partida-Martinez, L. P.; Peay, K. G.; Pelletier, D.; Peng, X.; Pester, M.; Pett-Ridge, J.; Peura, S.; Pjevac, P.; Plominsky, A. M.; Poehlein, A.; Pope, P. B.; Ravin, N.; Redmond, M. C.; Reiss, R.; Rich, V.; Rinke, C.; Rodrigues, J. L. M.; Rodriguez-Reillo, W.; Rossmassler, K.; Sackett, J.; Salekdeh, G. H.; Saleska, S.; Scarborough, M.; Schachtman, D.; Schadt, C. W.; Schrenk, M.; Sczyrba, A.; Sengupta, A.; Setubal, J. C.; Shade, A.; Sharp, C.; Sherman, D. H.; Shubenkova, O. V.; Sierra-Garcia, I. N.; Simister, R.; Simon, H.; Sjöling, S.; Slonczewski, J.; Correa de Souza, R. S.; Spear, J. R.; Stegen, J. C.; Stepanauskas, R.; Stewart, F.; Suen, G.; Sullivan, M.; Sumner, D.; Swan, B. K.; Swingley, W.; Tarn, J.; Taylor, G. T.; Teeling, H.; Tekere, M.; Teske, A.; Thomas, T.; Thrash, C.; Tiedje, J.; Ting, C. S.; Tully, B.; Tyson, G.; Ulloa, O.; Valentine, D. L.; Van Goethem, M. W.; VanderGheynst, J.; Verbeke, T. J.; Vollmers, J.; Vuillemin, A.; Waldo, N. B.; Walsh, D. A.; Weimer, B. C.; Whitman, T.; van der Wielen, P.; Wilkins, M.; Williams, T. J.; Woodcroft, B.; Woolet, J.; Wrighton, K.; Ye, J.; Young, E. B.; Youssef, N. H.; Yu, F. B.; Zemskaya, T. I.; Ziels, R.; Woyke, T.; Mouncey, N. J.; Ivanova, N. N.; Kyrpides, N. C.; Eloe-Fadrosh, E. A.; Consortium, Img M. Data

doi:10.1038/s41587-020-0718-6

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A genomic catalog of Earth’s microbiomes

Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., et al. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39(4), 499-509. doi:10.1038/s41587-020-0718-6.

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Item Permalink: https://hdl.handle.net/21.11116/0000-000A-A742-F Version Permalink: https://hdl.handle.net/21.11116/0000-000E-3A70-3

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https://doi.org/10.1038/s41587-020-0718-6 (Publisher version) Open Access Hybrid

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Nayfach, S., Author
Roux, S., Author
Seshadri, R., Author
Udwary, D., Author
Varghese, N., Author
Schulz, F., Author
Wu, D., Author
Paez-Espino, D., Author
Chen, I. M., Author
Huntemann, M., Author
Palaniappan, K., Author
Ladau, J., Author
Mukherjee, S., Author
Reddy, T. B. K., Author
Nielsen, T., Author
Kirton, E., Author
Faria, J. P., Author
Edirisinghe, J. N., Author
Henry, C. S., Author
Jungbluth, S. P., Author
Chivian, D., AuthorDehal, P., AuthorWood-Charlson, E. M., AuthorArkin, A. P., AuthorTringe, S. G., AuthorVisel, A., AuthorAbreu, H., AuthorAcinas, S. G., AuthorAllen, E., AuthorAllen, M. A., AuthorAlteio, L. V., AuthorAndersen, G., AuthorAnesio, A. M., AuthorAttwood, G., AuthorAvila-Magaña, V., AuthorBadis, Y., AuthorBailey, J., AuthorBaker, B., AuthorBaldrian, P., AuthorBarton, H. A., AuthorBeck, D. A. C., AuthorBecraft, E. D., AuthorBeller, H. R., AuthorBeman, J. M., AuthorBernier-Latmani, R., AuthorBerry, T. D., AuthorBertagnolli, A., AuthorBertilsson, S., AuthorBhatnagar, J. M., AuthorBird, J. T., AuthorBlanchard, J. L., AuthorBlumer-Schuette, S. E., AuthorBohannan, B., AuthorBorton, M. A., AuthorBrady, A., AuthorBrawley, S. H., AuthorBrodie, J., AuthorBrown, S., AuthorBrum, J. R., AuthorBrune, A.¹, Author Bryant, D. A., AuthorBuchan, A., AuthorBuckley, D. H., AuthorBuongiorno, J., AuthorCadillo-Quiroz, H., AuthorCaffrey, S. M., AuthorCampbell, A. N., AuthorCampbell, B., AuthorCarr, S., AuthorCarroll, J. L., AuthorCary, S. C., AuthorCates, A. M., AuthorCattolico, R. A., AuthorCavicchioli, R., AuthorChistoserdova, L., AuthorColeman, M. L., AuthorConstant, P., AuthorConway, J. M., AuthorMac Cormack, W. P., AuthorCrowe, S., AuthorCrump, B., AuthorCurrie, C., AuthorDaly, R., AuthorDeAngelis, K. M., AuthorDenef, V., AuthorDenman, S. E., AuthorDesta, A., AuthorDionisi, H., AuthorDodsworth, J., AuthorDombrowski, N., AuthorDonohue, T., AuthorDopson, M., AuthorDriscoll, T., AuthorDunfield, P., AuthorDupont, C. L., AuthorDynarski, K. A., AuthorEdgcomb, V., AuthorEdwards, E. A., AuthorElshahed, M. S., AuthorFigueroa, I., AuthorFlood, B., AuthorFortney, N., AuthorFortunato, C. S., AuthorFrancis, C., AuthorGachon, C. M. M., AuthorGarcia, S. L., AuthorGazitua, M. C., AuthorGentry, T., AuthorGerwick, L., AuthorGharechahi, J., AuthorGirguis, P., AuthorGladden, J., AuthorGradoville, M., AuthorGrasby, S. E., AuthorGravuer, K., AuthorGrettenberger, C. L., AuthorGruninger, R. J., AuthorGuo, J., AuthorHabteselassie, M. Y., AuthorHallam, S. J., AuthorHatzenpichler, R., AuthorHausmann, B., AuthorHazen, T. C., AuthorHedlund, B., AuthorHenny, C., AuthorHerfort, L., AuthorHernandez, M., AuthorHershey, O. S., AuthorHess, M., AuthorHollister, E. B., AuthorHug, L. A., AuthorHunt, D., AuthorJansson, J., AuthorJarett, J., AuthorKadnikov, V. V., AuthorKelly, C., AuthorKelly, R., AuthorKelly, W., AuthorKerfeld, C. A., AuthorKimbrel, J., AuthorKlassen, J. L., AuthorKonstantinidis, K. T., AuthorLee, L. L., AuthorLi, W. J., AuthorLoder, A. J., AuthorLoy, A., AuthorLozada, M., AuthorMacGregor, B., AuthorMagnabosco, C., AuthorMaria da Silva, A., AuthorMcKay, R. M., AuthorMcMahon, K., AuthorMcSweeney, C. S., AuthorMedina, M., AuthorMeredith, L., AuthorMizzi, J., AuthorMock, T., AuthorMomper, L., AuthorMoran, M. A., AuthorMorgan-Lang, C., AuthorMoser, D., AuthorMuyzer, G., AuthorMyrold, D., AuthorNash, M., AuthorNesbø, C. L., AuthorNeumann, A. P., AuthorNeumann, R. B., AuthorNoguera, D., AuthorNorthen, T., AuthorNorton, J., AuthorNowinski, B., AuthorNüsslein, K., AuthorO’Malley, M. A., AuthorOliveira, R. S., AuthorMaia de Oliveira, V., AuthorOnstott, T., AuthorOsvatic, J., AuthorOuyang, Y., AuthorPachiadaki, M., AuthorParnell, J., AuthorPartida-Martinez, L. P., AuthorPeay, K. G., AuthorPelletier, D., AuthorPeng, X., AuthorPester, M., AuthorPett-Ridge, J., AuthorPeura, S., AuthorPjevac, P., AuthorPlominsky, A. M., AuthorPoehlein, A., AuthorPope, P. B., AuthorRavin, N., AuthorRedmond, M. C., AuthorReiss, R., AuthorRich, V., AuthorRinke, C., AuthorRodrigues, J. L. M., AuthorRodriguez-Reillo, W., AuthorRossmassler, K., AuthorSackett, J., AuthorSalekdeh, G. H., AuthorSaleska, S., AuthorScarborough, M., AuthorSchachtman, D., AuthorSchadt, C. W., AuthorSchrenk, M., AuthorSczyrba, A., AuthorSengupta, A., AuthorSetubal, J. C., AuthorShade, A., AuthorSharp, C., AuthorSherman, D. H., AuthorShubenkova, O. V., AuthorSierra-Garcia, I. N., AuthorSimister, R., AuthorSimon, H., AuthorSjöling, S., AuthorSlonczewski, J., AuthorCorrea de Souza, R. S., AuthorSpear, J. R., AuthorStegen, J. C., AuthorStepanauskas, R., AuthorStewart, F., AuthorSuen, G., AuthorSullivan, M., AuthorSumner, D., AuthorSwan, B. K., AuthorSwingley, W., AuthorTarn, J., AuthorTaylor, G. T., AuthorTeeling, H., AuthorTekere, M., AuthorTeske, A., AuthorThomas, T., AuthorThrash, C., AuthorTiedje, J., AuthorTing, C. S., AuthorTully, B., AuthorTyson, G., AuthorUlloa, O., AuthorValentine, D. L., AuthorVan Goethem, M. W., AuthorVanderGheynst, J., AuthorVerbeke, T. J., AuthorVollmers, J., AuthorVuillemin, A., AuthorWaldo, N. B., AuthorWalsh, D. A., AuthorWeimer, B. C., AuthorWhitman, T., Authorvan der Wielen, P., AuthorWilkins, M., AuthorWilliams, T. J., AuthorWoodcroft, B., AuthorWoolet, J., AuthorWrighton, K., AuthorYe, J., AuthorYoung, E. B., AuthorYoussef, N. H., AuthorYu, F. B., AuthorZemskaya, T. I., AuthorZiels, R., AuthorWoyke, T., AuthorMouncey, N. J., AuthorIvanova, N. N., AuthorKyrpides, N. C., AuthorEloe-Fadrosh, E. A., AuthorConsortium, Img M. Data, Author more..

Affiliations:
1Department-Independent Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Max Planck Society, ou_3266271

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Free keywords: Agricultural robots Ecology Genes Metabolism Metabolites Viruses Agricultural soils Comparative analysis Engineered environments Interactive exploration Metabolic modeling Operational taxonomic units Phylogenetic diversity Secondary metabolites Bacteria archaeon article habitat human metagenome microbiome microorganism nonhuman sea soil virus animal bacterium classification ecosystem genetics isolation and purification metabolomics metagenomics microbiology phylogeny procedures publication Air Microbiology Animals Archaea Catalogs as Topic Humans Soil Microbiology Water Microbiology

Abstract: The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes. © 2020, The Author(s).

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Language(s): eng - English

Dates: Date issued: 2021

Publication Status: Issued

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Rev. Type: Peer

Identifiers: DOI: 10.1038/s41587-020-0718-6
ISSN: 10870156 (ISSN)

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Title: Nature Biotechnology

Abbreviation : Nat. Biotechnol.

Source Genre: Journal

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Publ. Info: New York : Gale Group Inc.

Pages: - Volume / Issue: 39 (4) Sequence Number: - Start / End Page: 499 - 509 Identifier: ISSN: 1087-0156
CoNE: https://pure.mpg.de/cone/journals/resource/954926980065