A communal catalogue reveals Earth’s multiscale microbial diversity

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, et al. (2017)
Nature 551(7681): 457-463.

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Autor*in
Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J.; Prill, Robert J.; Tripathi, Anupriya; Gibbons, Sean M.; Ackermann, Gail; Navas-Molina, Jose A.; Janssen, StefanUniBi
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Erscheinungsjahr
2017
Zeitschriftentitel
Nature
Band
551
Ausgabe
7681
Seite(n)
457-463
ISSN
0028-0836, 1476-4687
Page URI
https://pub.uni-bielefeld.de/record/2914868

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Thompson LR, Sanders JG, McDonald D, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551(7681):457-463.
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., et al. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), 457-463. https://doi.org/10.1038/nature24621
Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., et al. 2017. “A communal catalogue reveals Earth’s multiscale microbial diversity”. Nature 551 (7681): 457-463.
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). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457-463.
Thompson, L.R., et al., 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 551(7681), p 457-463.
L.R. Thompson, et al., “A communal catalogue reveals Earth’s multiscale microbial diversity”, Nature, vol. 551, 2017, pp. 457-463.
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., 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.L., 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.: A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 551, 457-463 (2017).
Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, 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, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jiří, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, 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., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, 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., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O'Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, 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., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia. “A communal catalogue reveals Earth’s multiscale microbial diversity”. Nature 551.7681 (2017): 457-463.

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Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions.
Petersen JM, Osvatic J., mSystems 3(2), 2018
PMID: 29556539
Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation.
Zhao S, Liu JJ, Banerjee S, Zhou N, Zhao ZY, Zhang K, Tian CY., Sci Rep 8(1), 2018
PMID: 29540760
The Madness of Microbiome: Attempting To Find Consensus "Best Practice" for 16S Microbiome Studies.
Pollock J, Glendinning L, Wisedchanwet T, Watson M., Appl Environ Microbiol 84(7), 2018
PMID: 29427429
In Search of Model Ecological Systems for Understanding Specialized Metabolism.
Pessotti RC, Hansen BL, Traxler MF., mSystems 3(2), 2018
PMID: 29629421
Introduction: The host-associated microbiome: Pattern, process and function.
Parfrey LW, Moreau CS, Russell JA., Mol Ecol 27(8), 2018
PMID: 29727917
The impact of vegan production on the kimchi microbiome.
Zabat MA, Sano WH, Cabral DJ, Wurster JI, Belenky P., Food Microbiol 74(), 2018
PMID: 29706333
Earth Microbiome Project and Global Systems Biology.
Gilbert JA, Jansson JK, Knight R., mSystems 3(3), 2018
PMID: 29657969
Chemical regulation of body feather microbiota in a wild bird.
Jacob S, Sallé L, Zinger L, Chaine AS, Ducamp C, Boutault L, Russell AF, Heeb P., Mol Ecol 27(7), 2018
PMID: 29533479
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.
Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R., mSystems 3(3), 2018
PMID: 29719869
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal.
Plewniak F, Crognale S, Rossetti S, Bertin PN., Front Microbiol 9(), 2018
PMID: 29755441
Ecological medicine.
Gilbert JA., Environ Microbiol 20(6), 2018
PMID: 29614208
Bacterial-fungal interactions: ecology, mechanisms and challenges.
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY., FEMS Microbiol Rev 42(3), 2018
PMID: 29471481
Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments.
Almeida A, Mitchell AL, Tarkowska A, Finn RD., Gigascience 7(5), 2018
PMID: 29762668
Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation.
Oliver A, Kay M, Cooper KK., BMC Genomics 19(1), 2018
PMID: 29716534
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere.
Simmons T, Caddell DF, Deng S, Coleman-Derr D., J Vis Exp (135), 2018
PMID: 29782021
Metagenome Sequences of Sediment from a Recovering Industrialized Appalachian River in West Virginia.
Huber DH, Ugwuanyi IR, Malkaram SA, Montenegro-Garcia NA, Lhilhi Noundou V, Chavarria-Palma JE., Genome Announc 6(18), 2018
PMID: 29724837
Gut microbiota utilize immunoglobulin A for mucosal colonization.
Donaldson GP, Ladinsky MS, Yu KB, Sanders JG, Yoo BB, Chou WC, Conner ME, Earl AM, Knight R, Bjorkman PJ, Mazmanian SK., Science 360(6390), 2018
PMID: 29724905
Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing.
O'Connell L, Gao S, McCorquodale D, Fleisher J, Lopez JV., PeerJ 6(), 2018
PMID: 29761039
What will it take to understand the ecology of symbiotic microorganisms?
Douglas AE., Environ Microbiol 20(6), 2018
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Microbial Community Analysis of Sauerkraut Fermentation Reveals a Stable and Rapidly Established Community.
Zabat MA, Sano WH, Wurster JI, Cabral DJ, Belenky P., Foods 7(5), 2018
PMID: 29757214
American Gut: an Open Platform for Citizen Science Microbiome Research.
McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, American Gut Consortium , Knight R., mSystems 3(3), 2018
PMID: 29795809
Standard methods for the assessment of structural and functional diversity of soil organisms: A review.
Römbke J, Bernard J, Martin-Laurent F., Integr Environ Assess Manag 14(4), 2018
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The social network of microorganisms - how auxotrophies shape complex communities.
Zengler K, Zaramela LS., Nat Rev Microbiol 16(6), 2018
PMID: 29599459
Environmental microbiology - the next 20 years: bioconnectivity and meta'omics 2.0.
Timmis K., Environ Microbiol 20(6), 2018
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The hunt for the most-wanted chemolithoautotrophic spookmicrobes.
In 't Zandt MH, de Jong AE, Slomp CP, Jetten MS., FEMS Microbiol Ecol 94(6), 2018
PMID: 29873717
Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.
Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS, Huang KC, Sonnenburg JL., Cell 173(7), 2018
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Quantifying Crop Rhizosphere Microbiome Ecology: The Next Frontier in Enhancing the Commercial Utility of Agricultural Microbes.
Zorner P, Farmer S, Alibek K., Ind Biotechnol (New Rochelle N Y) 14(3), 2018
PMID: 30083080
The gut microbiome of nonhuman primates: Lessons in ecology and evolution.
Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ., Am J Primatol 80(6), 2018
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Latent environment allocation of microbial community data.
Higashi K, Suzuki S, Kurosawa S, Mori H, Kurokawa K., PLoS Comput Biol 14(6), 2018
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A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation.
Mandalakis M, Panikov NS, Polymenakou PN, Sizova MV, Stamatakis A., Environ Sci Pollut Res Int 25(24), 2018
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Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition.
Hadrich D., Front Genet 9(), 2018
PMID: 29951086
Biogeography of soil bacteria and archaea across France.
Karimi B, Terrat S, Dequiedt S, Saby NPA, Horrigue W, Lelièvre M, Nowak V, Jolivet C, Arrouays D, Wincker P, Cruaud C, Bispo A, Maron PA, Bouré NCP, Ranjard L., Sci Adv 4(7), 2018
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Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry.
Zhalnina K, Zengler K, Newman D, Northen TR., MBio 9(4), 2018
PMID: 30018110
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units.
Glassman SI, Martiny JBH., mSphere 3(4), 2018
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Are microbiome studies ready for hypothesis-driven research?
Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R., Curr Opin Microbiol 44(), 2018
PMID: 30059804
Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol.
Dugas LR, Lie L, Plange-Rhule J, Bedu-Addo K, Bovet P, Lambert EV, Forrester TE, Luke A, Gilbert JA, Layden BT., BMC Public Health 18(1), 2018
PMID: 30081857
The Microbial Landscape of Sea Stars and the Anatomical and Interspecies Variability of Their Microbiome.
Jackson EW, Pepe-Ranney C, Debenport SJ, Buckley DH, Hewson I., Front Microbiol 9(), 2018
PMID: 30150973
Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function.
Ghuneim LJ, Jones DL, Golyshin PN, Golyshina OV., Front Microbiol 9(), 2018
PMID: 30186275
Species-Associated Differences in the Below-Ground Microbiomes of Wild and Domesticated Setaria.
Chaluvadi S, Bennetzen JL., Front Plant Sci 9(), 2018
PMID: 30186294
Metagenomic Approaches for Understanding New Concepts in Microbial Science.
Alves LF, Westmann CA, Lovate GL, de Siqueira GMV, Borelli TC, Guazzaroni ME., Int J Genomics 2018(), 2018
PMID: 30211213
Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).
Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R., Microbiologyopen 7(6), 2018
PMID: 30168288
Detecting eukaryotic microbiota with single-cell sensitivity in human tissue.
Lager S, de Goffau MC, Sovio U, Peacock SJ, Parkhill J, Charnock-Jones DS, Smith GCS., Microbiome 6(1), 2018
PMID: 30172254
A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms.
Hernandez-Agreda A, Leggat W, Ainsworth TD., Front Microbiol 9(), 2018
PMID: 30245683
The Rootstock Regulates Microbiome Diversity in Root and Rhizosphere Compartments of Vitis vinifera Cultivar Lambrusco.
D'Amico F, Candela M, Turroni S, Biagi E, Brigidi P, Bega A, Vancini D, Rampelli S., Front Microbiol 9(), 2018
PMID: 30319569
Clinician Guide to Microbiome Testing.
Staley C, Kaiser T, Khoruts A., Dig Dis Sci 63(12), 2018
PMID: 30267172
Qiita: rapid, web-enabled microbiome meta-analysis.
Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R., Nat Methods 15(10), 2018
PMID: 30275573
Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis.
Maricic I, Marrero I, Eguchi A, Nakamura R, Johnson CD, Dasgupta S, Hernandez CD, Nguyen PS, Swafford AD, Knight R, Feldstein AE, Loomba R, Kumar V., J Immunol 201(10), 2018
PMID: 30322964
From hairballs to hypotheses-biological insights from microbial networks.
Röttjers L, Faust K., FEMS Microbiol Rev 42(6), 2018
PMID: 30085090
Interaction between ferruginous clay sediment and an iron-reducing hyperthermophilic Pyrobaculum sp. in a terrestrial hot spring.
Stewart LC, Houghton K, Carere CR, Power JF, Chambefort I, Stott MB., FEMS Microbiol Ecol 94(11), 2018
PMID: 30124835
High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.
Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R., mSystems 3(6), 2018
PMID: 30417111
Identifying and Predicting Novelty in Microbiome Studies.
Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J., MBio 9(6), 2018
PMID: 30425147
Evaluating the Information Content of Shallow Shotgun Metagenomics.
Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D., mSystems 3(6), 2018
PMID: 30443602
Reevaluating the Salty Divide: Phylogenetic Specificity of Transitions between Marine and Freshwater Systems.
Paver SF, Muratore D, Newton RJ, Coleman ML., mSystems 3(6), 2018
PMID: 30443603
The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus.
Vrbanac A, Riestra AM, Coady A, Knight R, Nizet V, Patras KA., BMC Microbiol 18(1), 2018
PMID: 30477439
SEDE-GPS: socio-economic data enrichment based on GPS information.
Sperlea T, Füser S, Boenigk J, Heider D., BMC Bioinformatics 19(suppl 15), 2018
PMID: 30497363
Community profiling of the urinary microbiota: considerations for low-biomass samples.
Karstens L, Asquith M, Caruso V, Rosenbaum JT, Fair DA, Braun J, Gregory WT, Nardos R, McWeeney SK., Nat Rev Urol 15(12), 2018
PMID: 30315209
Gut microbial features can predict host phenotype response to protein deficiency.
Navarro G, Sharma A, Dugas LR, Forrester T, Gilbert JA, Layden BT., Physiol Rep 6(23), 2018
PMID: 30516001
A practical introduction to microbial molecular ecology through the use of isolation chips.
Alessi AM, Redeker KR, Chong JPJ., Ecol Evol 8(24), 2018
PMID: 30619545
Identification of Microbial Dark Matter in Antarctic Environments.
Bowman JS., Front Microbiol 9(), 2018
PMID: 30619224

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McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG., Gigascience 1(1), 2012
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Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.
Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM, Chase J, McDonald D, Gonzalez A, Robbins-Pianka A, Clemente JC, Gilbert JA, Huse SM, Zhou HW, Knight R, Caporaso JG., PeerJ 2(), 2014
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Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.
Hamady M, Lozupone C, Knight R., ISME J 4(1), 2009
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SEPP: SATe-enabled phylogenetic placement.
Mirarab S, Nguyen N, Warnow T., Pac Symp Biocomput (), 2012
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EMPeror: a tool for visualizing high-throughput microbial community data.
Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R., Gigascience 2(1), 2013
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Uberon, an integrative multi-species anatomy ontology.
Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA., Genome Biol. 13(1), 2012
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The plant ontology as a tool for comparative plant anatomy and genomic analyses.
Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P., Plant Cell Physiol. 54(2), 2012
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An ontology for microbial phenotypes.
Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG., BMC Microbiol. 14(), 2014
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QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
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SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Kopylova E, Noe L, Touzet H., Bioinformatics 28(24), 2012
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Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.
Schloss PD, Gevers D, Westcott SL., PLoS ONE 6(12), 2011
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VSEARCH: a versatile open source tool for metagenomics.
Rognes T, Flouri T, Nichols B, Quince C, Mahe F., PeerJ 4(), 2016
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A new generation of homology search tools based on probabilistic inference.
Eddy SR., Genome Inform 23(1), 2009
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pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A., Bioinformatics 30(9), 2014
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Cython: the best of both worlds
AUTHOR UNKNOWN, 2011

AUTHOR UNKNOWN, 2016
Simple and efficient fully-functional succinct trees
AUTHOR UNKNOWN, 2016
A mathematical theory of communication
AUTHOR UNKNOWN, 1948
Nonparametric estimation of the number of classes in a population
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Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories.
Guo W, Sarkar SK, Peddada SD., Biometrics 66(2), 2009
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A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies
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vegan: Community Ecology Package
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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.
Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C., Nat. Biotechnol. 31(9), 2013
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Building predictive models in R using the caret package
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Classification and regression by randomForest
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Bayesian community-wide culture-independent microbial source tracking.
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST., Nat. Methods 8(9), 2011
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A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement
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A consumer’s guide to nestedness analysis
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Ribosomal Database Project: data and tools for high throughput rRNA analysis.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM., Nucleic Acids Res. 42(Database issue), 2013
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Pasteurella multocida--the major cause of hand infections following domestic animal bites.
Arons MS, Fernando L, Polayes IM., J Hand Surg Am 7(1), 1982
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Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals.
Ormerod KL, Wood DL, Lachner N, Gellatly SL, Daly JN, Parsons JD, Dal'Molin CG, Palfreyman RW, Nielsen LK, Cooper MA, Morrison M, Hansbro PM, Hugenholtz P., Microbiome 4(1), 2016
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