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Title: A communal catalogue reveals Earth’s multiscale microbial diversity

Abstract

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.

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; W.M. Keck Foundation; National Science Foundation (NSF); Australian Research Council; National Oceanic and Atmospheric Administration (NOAA)
Contributing Org.:
The Earth Microbiome Project Consortium
OSTI Identifier:
1411914
Alternate Identifier(s):
OSTI ID: 1467890
Report Number(s):
PNNL-SA-123888
Journal ID: ISSN 0028-0836
Grant/Contract Number:  
AC05-76RL01830; AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 551; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; microbiome; Earth; global; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

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, Jirˇí, 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. United States: N. p., 2017. Web. doi:10.1038/nature24621.
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, Jirˇí, 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, & Zhao, Hongxia. A communal catalogue reveals Earth’s multiscale microbial diversity. United States. https://doi.org/10.1038/nature24621
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, Jirˇí, 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. Wed . "A communal catalogue reveals Earth’s multiscale microbial diversity". United States. https://doi.org/10.1038/nature24621. https://www.osti.gov/servlets/purl/1411914.
@article{osti_1411914,
title = {A communal catalogue reveals Earth’s multiscale microbial diversity},
author = {Thompson, Luke R. and Sanders, Jon G. and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J. and Prill, Robert J. and Tripathi, Anupriya and Gibbons, Sean M. and Ackermann, Gail and Navas-Molina, Jose A. and Janssen, Stefan and Kopylova, Evguenia and Vázquez-Baeza, Yoshiki and González, Antonio and Morton, James T. and Mirarab, Siavash and Zech Xu, Zhenjiang and Jiang, Lingjing and Haroon, Mohamed F. and Kanbar, Jad and Zhu, Qiyun and Jin Song, Se and Kosciolek, Tomasz and Bokulich, Nicholas A. and Lefler, Joshua and Brislawn, Colin J. and Humphrey, Gregory and Owens, Sarah M. and Hampton-Marcell, Jarrad and Berg-Lyons, Donna and McKenzie, Valerie and Fierer, Noah and Fuhrman, Jed A. and Clauset, Aaron and Stevens, Rick L. and Shade, Ashley and Pollard, Katherine S. and Goodwin, Kelly D. and Jansson, Janet K. and Gilbert, Jack A. and Knight, Rob and Rivera, Jose L. Agosto and Al-Moosawi, Lisa and Alverdy, John and Amato, Katherine R. and Andras, Jason and Angenent, Largus T. and Antonopoulos, Dionysios A. and Apprill, Amy and Armitage, David and Ballantine, Kate and Bárta, Jirˇí and Baum, Julia K. and Berry, Allison and Bhatnagar, Ashish and Bhatnagar, Monica and Biddle, Jennifer F. and Bittner, Lucie and Boldgiv, Bazartseren and Bottos, Eric and Boyer, Donal M. and Braun, Josephine and Brazelton, William and Brearley, Francis Q. and Campbell, Alexandra H. and Caporaso, J. Gregory and Cardona, Cesar and Carroll, JoLynn and Cary, S. Craig and Casper, Brenda B. and Charles, Trevor C. and Chu, Haiyan and Claar, Danielle C. and Clark, Robert G. and Clayton, Jonathan B. and Clemente, Jose C. and Cochran, Alyssa and Coleman, Maureen L. and Collins, Gavin and Colwell, Rita R. and Contreras, Mónica and Crary, Benjamin B. and Creer, Simon and Cristol, Daniel A. and Crump, Byron C. and Cui, Duoying and Daly, Sarah E. and Davalos, Liliana and Dawson, Russell D. and Defazio, Jennifer and Delsuc, Frédéric and Dionisi, Hebe M. and Dominguez-Bello, Maria Gloria and Dowell, Robin and Dubinsky, Eric A. and Dunn, Peter O. and Ercolini, Danilo and Espinoza, Robert E. and Ezenwa, Vanessa and Fenner, Nathalie and Findlay, Helen S. and Fleming, Irma D. and Fogliano, Vincenzo and Forsman, Anna and Freeman, Chris and Friedman, Elliot S. and Galindo, Giancarlo and Garcia, Liza and Garcia-Amado, Maria Alexandra and Garshelis, David and Gasser, Robin B. and Gerdts, Gunnar and Gibson, Molly K. and Gifford, Isaac and Gill, Ryan T. and Giray, Tugrul and Gittel, Antje and Golyshin, Peter and Gong, Donglai and Grossart, Hans-Peter and Guyton, Kristina and Haig, Sarah-Jane and Hale, Vanessa and Hall, Ross Stephen and Hallam, Steven J. and Handley, Kim M. and Hasan, Nur A. and Haydon, Shane R. and Hickman, Jonathan E. and Hidalgo, Glida and Hofmockel, Kirsten S. and Hooker, Jeff and Hulth, Stefan and Hultman, Jenni and Hyde, Embriette and Ibáñez-Álamo, Juan Diego and Jastrow, Julie D. and Jex, Aaron R. and Johnson, L. Scott and Johnston, Eric R. and Joseph, Stephen and Jurburg, Stephanie D. and Jurelevicius, Diogo and Karlsson, Anders and Karlsson, Roger and Kauppinen, Seth and Kellogg, Colleen T. E. and Kennedy, Suzanne J. and Kerkhof, Lee J. and King, Gary M. and Kling, George W. and Koehler, Anson V. and Krezalek, Monika and Kueneman, Jordan and Lamendella, Regina and Landon, Emily M. and Lane-deGraaf, Kelly and LaRoche, Julie and Larsen, Peter and Laverock, Bonnie and Lax, Simon and Lentino, Miguel and Levin, Iris I. and Liancourt, Pierre and Liang, Wenju and Linz, Alexandra M. and Lipson, David A. and Liu, Yongqin and Lladser, Manuel E. and Lozada, Mariana and Spirito, Catherine M. and MacCormack, Walter P. and MacRae-Crerar, Aurora and Magris, Magda and Martín-Platero, Antonio M. and Martín-Vivaldi, Manuel and Martínez, L. Margarita and Martínez-Bueno, Manuel and Marzinelli, Ezequiel M. and Mason, Olivia U. and Mayer, Gregory D. and McDevitt-Irwin, Jamie M. and McDonald, James E. and McGuire, Krista L. and McMahon, Katherine D. and McMinds, Ryan and Medina, Mónica and Mendelson, Joseph R. and Metcalf, Jessica L. and Meyer, Folker and Michelangeli, Fabian and Miller, Kim and Mills, David A. and Minich, Jeremiah and Mocali, Stefano and Moitinho-Silva, Lucas and Moore, Anni and Morgan-Kiss, Rachael M. and Munroe, Paul and Myrold, David and Neufeld, Josh D. and Ni, Yingying and Nicol, Graeme W. and Nielsen, Shaun and Nissimov, Jozef I. and Niu, Kefeng and Nolan, Matthew J. and Noyce, Karen and O’Brien, Sarah L. and Okamoto, Noriko and Orlando, Ludovic and Castellano, Yadira Ortiz and Osuolale, Olayinka and Oswald, Wyatt and Parnell, Jacob and Peralta-Sánchez, Juan M. and Petraitis, Peter and Pfister, Catherine and Pilon-Smits, Elizabeth and Piombino, Paola and Pointing, Stephen B. and Pollock, F. Joseph and Potter, Caitlin and Prithiviraj, Bharath and Quince, Christopher and Rani, Asha and Ranjan, Ravi and Rao, Subramanya and Rees, Andrew P. and Richardson, Miles and Riebesell, Ulf and Robinson, Carol and Rockne, Karl J. and Rodriguezl, Selena Marie and Rohwer, Forest and Roundstone, Wayne and Safran, Rebecca J. and Sangwan, Naseer and Sanz, Virginia and Schrenk, Matthew and Schrenzel, Mark D. and Scott, Nicole M. and Seger, Rita L. and Seguin-Orlando, Andaine and Seldin, Lucy and Seyler, Lauren M. and Shakhsheer, Baddr and Sheets, Gabriela M. and Shen, Congcong and Shi, Yu and Shin, Hakdong and Shogan, Benjamin D. and Shutler, Dave and Siegel, Jeffrey and Simmons, Steve and Sjöling, Sara and Smith, Daniel P. and Soler, Juan J. and Sperling, Martin and Steinberg, Peter D. and Stephens, Brent and Stevens, Melita A. and Taghavi, Safiyh and Tai, Vera and Tait, Karen and Tan, Chia L. and Tas¸, Neslihan and Taylor, D. Lee and Thomas, Torsten and Timling, Ina and Turner, Benjamin L. and Urich, Tim and Ursell, Luke K. and van der Lelie, Daniel and Van Treuren, William and van Zwieten, Lukas and Vargas-Robles, Daniela and Thurber, Rebecca Vega and Vitaglione, Paola and Walker, Donald A. and Walters, William A. and Wang, Shi and Wang, Tao and Weaver, Tom and Webster, Nicole S. and Wehrle, Beck and Weisenhorn, Pamela and Weiss, Sophie and Werner, Jeffrey J. and West, Kristin and Whitehead, Andrew and Whitehead, Susan R. and Whittingham, Linda A. and Willerslev, Eske and Williams, Allison E. and Wood, Stephen A. and Woodhams, Douglas C. and Yang, Yeqin and Zaneveld, Jesse and Zarraonaindia, Iratxe and Zhang, Qikun and Zhao, Hongxia},
abstractNote = {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.},
doi = {10.1038/nature24621},
journal = {Nature (London)},
number = ,
volume = 551,
place = {United States},
year = {2017},
month = {11}
}

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Figures / Tables:

Figure 1 | Environment type and provenance of samples. Figure 1 | Environment type and provenance of samples.: a, The EMP ontology (EMPO) classifies microbial environments (level 3) as free-living or host-associated (level 1) and saline or non-saline (if free-living) or animal or plant (if host-associated) (level 2). The number out of 23,828 samples in the QC-filtered subsetmore » in each environment is provided. EMPO is described with examples at http://www.earthmicrobiome.org/protocolsand- standards/empo. b, Global scope of sample provenance: samples come from 7 continents, 43 countries, 21 biomes (ENVO), 92 environmental features (ENVO), and 17 environments (EMPO).« less

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Works referenced in this record:

A Mathematical Theory of Communication
journal, July 1948


Global patterns in bacterial diversity
journal, June 2007

  • Lozupone, C. A.; Knight, R.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 27
  • DOI: 10.1073/pnas.0611525104

Uberon, an integrative multi-species anatomy ontology
journal, January 2012

  • Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V.
  • Genome Biology, Vol. 13, Issue 1
  • DOI: 10.1186/gb-2012-13-1-r5

Microbial diversity in the deep sea and the underexplored "rare biosphere"
journal, July 2006

  • Sogin, M. L.; Morrison, H. G.; Huber, J. A.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 32
  • DOI: 10.1073/pnas.0605127103

A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies
journal, February 2016


Determinants of community structure in the global plankton interactome
journal, May 2015


Decreases in average bacterial community rRNA operon copy number during succession
journal, November 2015

  • Nemergut, Diana R.; Knelman, Joseph E.; Ferrenberg, Scott
  • The ISME Journal, Vol. 10, Issue 5
  • DOI: 10.1038/ismej.2015.191

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
journal, July 2016

  • Gohl, Daryl M.; Vangay, Pajau; Garbe, John
  • Nature Biotechnology, Vol. 34, Issue 9
  • DOI: 10.1038/nbt.3601

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys
journal, December 2015


Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
journal, August 2013

  • Langille, Morgan G. I.; Zaneveld, Jesse; Caporaso, J. Gregory
  • Nature Biotechnology, Vol. 31, Issue 9
  • DOI: 10.1038/nbt.2676

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
journal, May 2011

  • Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn
  • Nature Biotechnology, Vol. 29, Issue 5
  • DOI: 10.1038/nbt.1823

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
journal, December 2011

  • McDonald, Daniel; Price, Morgan N.; Goodrich, Julia
  • The ISME Journal, Vol. 6, Issue 3
  • DOI: 10.1038/ismej.2011.139

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
journal, January 2010

  • Gilbert, Jack A.; Meyer, Folker; Antonopoulos, Dion
  • Standards in Genomic Sciences, Vol. 3, Issue 3
  • DOI: 10.4056/sigs.1433550

Quantifying human impact on Earth's microbiome
journal, August 2016


A consumer's guide to nestedness analysis
journal, January 2009


Worlds within worlds: evolution of the vertebrate gut microbiota
journal, October 2008

  • Ley, Ruth E.; Lozupone, Catherine A.; Hamady, Micah
  • Nature Reviews Microbiology, Vol. 6, Issue 10
  • DOI: 10.1038/nrmicro1978

The environment ontology: contextualising biological and biomedical entities
journal, January 2013

  • Buttigieg, Pier; Morrison, Norman; Smith, Barry
  • Journal of Biomedical Semantics, Vol. 4, Issue 1
  • DOI: 10.1186/2041-1480-4-43

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem
journal, March 2017


Global marine bacterial diversity peaks at high latitudes in winter
journal, March 2013

  • Ladau, Joshua; Sharpton, Thomas J.; Finucane, Mariel M.
  • The ISME Journal, Vol. 7, Issue 9
  • DOI: 10.1038/ismej.2013.37

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010

  • Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
  • DOI: 10.1073/pnas.1000080107

Investigating causality of nestedness of insular communities: selective immigrations or extinctions?
journal, September 1996


The Earth Microbiome project: successes and aspirations
journal, August 2014


Ironing out the wrinkles in the rare biosphere through improved OTU clustering: Ironing out the wrinkles in the rare biosphere
journal, March 2010


Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton
journal, June 2015

  • Apprill, A.; McNally, S.; Parsons, R.
  • Aquatic Microbial Ecology, Vol. 75, Issue 2
  • DOI: 10.3354/ame01753

Simple and efficient fully-functional succinct trees
journal, December 2016


Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014


Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
journal, January 2014

  • Rideout, Jai Ram; He, Yan; Navas-Molina, Jose A.
  • PeerJ, Vol. 2
  • DOI: 10.7717/peerj.545

A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement
journal, August 2008


Ribosomal Database Project: data and tools for high throughput rRNA analysis
journal, November 2013

  • Cole, James R.; Wang, Qiong; Fish, Jordan A.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1244

Conservation evaluation and phylogenetic diversity
journal, January 1992


Microbial Ecology and Evolution: A Ribosomal RNA Approach
journal, October 1986


The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
journal, December 2012

  • Cooper, Laurel; Walls, Ramona L.; Elser, Justin
  • Plant and Cell Physiology, Vol. 54, Issue 2
  • DOI: 10.1093/pcp/pcs163

Consistently inconsistent drivers of microbial diversity and abundance at macroecological scales
journal, June 2017

  • Hendershot, John Nicholas; Read, Quentin D.; Henning, Jeremiah A.
  • Ecology, Vol. 98, Issue 7
  • DOI: 10.1002/ecy.1829

Marine bacterial, archaeal and protistan association networks reveal ecological linkages
journal, March 2011

  • Steele, Joshua A.; Countway, Peter D.; Xia, Li
  • The ISME Journal, Vol. 5, Issue 9
  • DOI: 10.1038/ismej.2011.24

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014


Going back to the roots: the microbial ecology of the rhizosphere
journal, September 2013

  • Philippot, Laurent; Raaijmakers, Jos M.; Lemanceau, Philippe
  • Nature Reviews Microbiology, Vol. 11, Issue 11
  • DOI: 10.1038/nrmicro3109

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

  • Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1219

Building Predictive Models in R Using the caret Package
journal, January 2008


An ontology for microbial phenotypes
journal, November 2014

  • Chibucos, Marcus C.; Zweifel, Adrienne E.; Herrera, Jonathan C.
  • BMC Microbiology, Vol. 14, Issue 1
  • DOI: 10.1186/s12866-014-0294-3

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation
journal, September 2016

  • Buttigieg, Pier Luigi; Pafilis, Evangelos; Lewis, Suzanna E.
  • Journal of Biomedical Semantics, Vol. 7, Issue 1
  • DOI: 10.1186/s13326-016-0097-6

Pasteurella multocida—The major cause of hand infections following domestic animal bites
journal, January 1982


SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
journal, October 2012


Low diversity of planktonic bacteria in the tropical ocean
journal, January 2016

  • Milici, Mathias; Tomasch, Jürgen; Wos-Oxley, Melissa L.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep19054

Spatial Gaps in Global Biodiversity Information and the Role of 
Citizen Science
journal, March 2016

  • Amano, Tatsuya; Lamming, James D. L.; Sutherland, William J.
  • BioScience, Vol. 66, Issue 5
  • DOI: 10.1093/biosci/biw022

VSEARCH: a versatile open source tool for metagenomics
journal, January 2016


The measure of order and disorder in the distribution of species in fragmented habitat
journal, December 1993


Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
journal, February 2016


The founding charter of the Genomic Observatories Network
journal, March 2014

  • Davies, Neil; Field, Dawn; Amaral-Zettler, Linda
  • GigaScience, Vol. 3, Issue 1
  • DOI: 10.1186/2047-217X-3-2

Measuring fractions of beta diversity and their relationships to nestedness: a theoretical and empirical comparison of novel approaches
journal, September 2012


A new view of the tree of life
journal, April 2016


The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
journal, July 2012

  • McDonald, Daniel; Clemente, Jose C.; Kuczynski, Justin
  • GigaScience, Vol. 1, Issue 1
  • DOI: 10.1186/2047-217X-1-7

A meta-analysis of changes in bacterial and archaeal communities with time
journal, April 2013

  • Shade, Ashley; Gregory Caporaso, J.; Handelsman, Jo
  • The ISME Journal, Vol. 7, Issue 8
  • DOI: 10.1038/ismej.2013.54

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
journal, August 2009

  • Hamady, Micah; Lozupone, Catherine; Knight, Rob
  • The ISME Journal, Vol. 4, Issue 1
  • DOI: 10.1038/ismej.2009.97

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes: Bacterial biogeography in arctic soils
journal, November 2010


Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals
journal, July 2016


rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria
journal, April 2000


pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
journal, October 2010

  • Matsen, Frederick A.; Kodner, Robin B.; Armbrust, E. Virginia
  • BMC Bioinformatics, Vol. 11, Issue 1
  • DOI: 10.1186/1471-2105-11-538

The diversity and biogeography of soil bacterial communities
journal, January 2006

  • Fierer, N.; Jackson, R. B.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 3
  • DOI: 10.1073/pnas.0507535103

Temperature mediates continental-scale diversity of microbes in forest soils
journal, July 2016

  • Zhou, Jizhong; Deng, Ye; Shen, Lina
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12083

Cython: The Best of Both Worlds
journal, March 2011

  • Behnel, Stefan; Bradshaw, Robert; Citro, Craig
  • Computing in Science & Engineering, Vol. 13, Issue 2
  • DOI: 10.1109/MCSE.2010.118

A unified initiative to harness Earth's microbiomes
journal, October 2015


Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012

  • Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
  • The ISME Journal, Vol. 6, Issue 8
  • DOI: 10.1038/ismej.2012.8

EMPeror: a tool for visualizing high-throughput microbial community data
journal, November 2013

  • Vázquez-Baeza, Yoshiki; Pirrung, Meg; Gonzalez, Antonio
  • GigaScience, Vol. 2, Issue 1
  • DOI: 10.1186/2047-217X-2-16

Diet-induced extinctions in the gut microbiota compound over generations
journal, January 2016

  • Sonnenburg, Erica D.; Smits, Samuel A.; Tikhonov, Mikhail
  • Nature, Vol. 529, Issue 7585
  • DOI: 10.1038/nature16504

On the Generality of the Latitudinal Diversity Gradient
journal, February 2004

  • Hillebrand, Helmut
  • The American Naturalist, Vol. 163, Issue 2
  • DOI: 10.1086/381004

Bayesian community-wide culture-independent microbial source tracking
journal, July 2011

  • Knights, Dan; Kuczynski, Justin; Charlson, Emily S.
  • Nature Methods, Vol. 8, Issue 9
  • DOI: 10.1038/nmeth.1650

A latitudinal diversity gradient in planktonic marine bacteria
journal, May 2008

  • Fuhrman, J. A.; Steele, J. A.; Hewson, I.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 22
  • DOI: 10.1073/pnas.0803070105

Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss
journal, April 2014


Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
journal, December 2011


DNA Sequencing as a Tool to Monitor Marine Ecological Status
journal, May 2017

  • Goodwin, Kelly D.; Thompson, Luke R.; Duarte, Bernardo
  • Frontiers in Marine Science, Vol. 4
  • DOI: 10.3389/fmars.2017.00107

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
journal, July 2017

  • Callahan, Benjamin J.; McMurdie, Paul J.; Holmes, Susan P.
  • The ISME Journal, Vol. 11, Issue 12
  • DOI: 10.1038/ismej.2017.119

A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity [Supplemental Data]
dataset, November 2017

  • Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel
  • Zenodo-Supplementary information for journal article at DOI: 10.1038/nature24621, 33 files (47.3 GB)
  • DOI: 10.5281/zenodo.890000

A communal catalogue reveals Earth's multiscale microbial diversity
dataset, November 2017

  • Thompson, Luke; Sanders, Jon; McDonald, Daniel
  • Zenodo, 33 files (CSV, TSV, BIOM, TXT, GZ, RDB); 47.3 GB
  • DOI: 10.5281/zenodo.889999

Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula
journal, June 2020


The Gut Microbiome in Autism: Study-Site Effects and Longitudinal Analysis of Behavior Change
journal, April 2021


Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
text, January 2014

  • Salter, Susannah; Cox, Michael J.; Turek, Elena M.
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.41109

A Mathematical Theory of Communication
journal, October 1948


pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution
text, January 2017

  • Jun, Zeng,; Xiangui, Lin,; Qinghe, Zhu,
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/7hnn-ek45

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
preprint, January 2010


VSEARCH: a versatile open source tool for metagenomics
text, January 2016


Works referencing / citing this record:

Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing
journal, January 2020

  • Selway, Caitlin A.; Eisenhofer, Raphael; Weyrich, Laura S.
  • The Journal of Pathology: Clinical Research, Vol. 6, Issue 2
  • DOI: 10.1002/cjp2.151

Structural changes of the microplankton community following a pulse of inorganic nitrogen in a eutrophic river
journal, January 2020

  • Kleinteich, Julia; Hilt, Sabine; Hoppe, Andreas
  • Limnology and Oceanography, Vol. 65, Issue S1
  • DOI: 10.1002/lno.11352

Evaluation of accuracy and precision in an amplicon sequencing workflow for marine protist communities
journal, December 2019

  • Catlett, Dylan; Matson, Paul G.; Carlson, Craig A.
  • Limnology and Oceanography: Methods, Vol. 18, Issue 1
  • DOI: 10.1002/lom3.10343

Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses
journal, April 2019


Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
journal, February 2020


Salt Marsh Greenhouse Gas Fluxes and Microbial Communities Are Not Sensitive to the First Year of Precipitation Change
journal, May 2019

  • Emery, Hollie E.; Angell, John H.; Fulweiler, R. W.
  • Journal of Geophysical Research: Biogeosciences, Vol. 124, Issue 5
  • DOI: 10.1029/2018jg004788

Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide
journal, March 2019


How sample heterogeneity can obscure the signal of microbial interactions
journal, June 2019


TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
journal, May 2019


Bacterial adaptation is constrained in complex communities
journal, February 2020


Bacterial diversification through geological time
journal, July 2018

  • Louca, Stilianos; Shih, Patrick M.; Pennell, Matthew W.
  • Nature Ecology & Evolution, Vol. 2, Issue 9
  • DOI: 10.1038/s41559-018-0625-0

Community richness of amphibian skin bacteria correlates with bioclimate at the global scale
journal, February 2019

  • Kueneman, Jordan G.; Bletz, Molly C.; McKenzie, Valerie J.
  • Nature Ecology & Evolution, Vol. 3, Issue 3
  • DOI: 10.1038/s41559-019-0798-1

Transmission of human-associated microbiota along family and social networks
journal, March 2019


Community profiling of the urinary microbiota: considerations for low-biomass samples
journal, October 2018


Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
journal, May 2019


Striped UniFrac: enabling microbiome analysis at unprecedented scale
journal, October 2018

  • McDonald, Daniel; Vázquez-Baeza, Yoshiki; Koslicki, David
  • Nature Methods, Vol. 15, Issue 11
  • DOI: 10.1038/s41592-018-0187-8

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling
journal, July 2019


Nutrient-based diet modifications impact on the gut microbiome of the Javan slow loris (Nycticebus javanicus)
journal, March 2019


Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study
journal, February 2020

  • Burcham, Zachary M.; Garneau, Nicole L.; Comstock, Sarah S.
  • Scientific Reports, Vol. 10, Issue 1
  • DOI: 10.1038/s41598-020-59016-0

A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns
journal, February 2020


Restoring subtidal marine macrophytes in the Anthropocene: trajectories and future-proofing
journal, January 2019

  • Wood, G.; Marzinelli, E. M.; Coleman, M. A.
  • Marine and Freshwater Research, Vol. 70, Issue 7
  • DOI: 10.1071/mf18226

Changes in bacterial community composition across natural grassland and pine forests in the Bunya Mountains in subtropical Australia
journal, January 2019

  • Shen, Ju-Pei; Esfandbod, Maryam; Wakelin, Steve A.
  • Soil Research, Vol. 57, Issue 8
  • DOI: 10.1071/sr19111

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments
journal, February 2018

  • Burghardt, Liana T.; Epstein, Brendan; Guhlin, Joseph
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 10
  • DOI: 10.1073/pnas.1714246115

Redox traits characterize the organization of global microbial communities
journal, February 2019

  • Ramírez-Flandes, Salvador; González, Bernardo; Ulloa, Osvaldo
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 9
  • DOI: 10.1073/pnas.1817554116

Chemical and microbial diversity covary in fresh water to influence ecosystem functioning
journal, November 2019

  • Tanentzap, Andrew J.; Fitch, Amelia; Orland, Chloe
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 49
  • DOI: 10.1073/pnas.1904896116

Initial Evidence of the Relationships between the Human Postmortem Microbiome and Neighborhood Blight and Greening Efforts
journal, February 2019

  • Pearson, Amber L.; Rzotkiewicz, Amanda; Pechal, Jennifer L.
  • Annals of the American Association of Geographers, Vol. 109, Issue 3
  • DOI: 10.1080/24694452.2018.1519407

Methods for automatic reference trees and multilevel phylogenetic placement
journal, August 2018


Rapid alignment-free phylogenetic identification of metagenomic sequences
journal, January 2019


Interaction between ferruginous clay sediment and an iron-reducing hyperthermophilic Pyrobaculum sp. in a terrestrial hot spring
journal, August 2018

  • Stewart, Lucy C.; Houghton, Karen; Carere, Carlo R.
  • FEMS Microbiology Ecology, Vol. 94, Issue 11
  • DOI: 10.1093/femsec/fiy160

Inevitable future: space colonization beyond Earth with microbes first
journal, August 2019

  • Lopez, Jose V.; Peixoto, Raquel S.; Rosado, Alexandre S.
  • FEMS Microbiology Ecology, Vol. 95, Issue 10
  • DOI: 10.1093/femsec/fiz127

Untapped sponge microbiomes: structure specificity at host order and family levels
journal, August 2019

  • Yang, Qi; Franco, Christopher M. M.; Lin, Hou-Wen
  • FEMS Microbiology Ecology, Vol. 95, Issue 9
  • DOI: 10.1093/femsec/fiz136

HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes
journal, February 2020


Host identity and symbiotic association affects the taxonomic and functional diversity of the clownfish-hosting sea anemone microbiome
journal, February 2020

  • Titus, Benjamin M.; Laroche, Robert; Rodríguez, Estefanía
  • Biology Letters, Vol. 16, Issue 2
  • DOI: 10.1098/rsbl.2019.0738

Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14
journal, February 2020

  • Kochetkova, Tatiana V.; Zayulina, Kseniya S.; Zhigarkov, Vyacheslav S.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2
  • DOI: 10.1099/ijsem.0.003902

Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
journal, July 2018


Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units
journal, July 2018


In Search of Model Ecological Systems for Understanding Specialized Metabolism
journal, March 2018


redbiom: a Rapid Sample Discovery and Feature Characterization System
journal, June 2019


Earth Microbiome Project and Global Systems Biology
journal, April 2018


Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes
journal, September 2019


SEDE-GPS: socio-economic data enrichment based on GPS information
journal, November 2018


AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
journal, November 2019


Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol
journal, August 2018


An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men
journal, November 2018

  • Armstrong, Abigail J. S.; Shaffer, Michael; Nusbacher, Nichole M.
  • Microbiome, Vol. 6, Issue 1
  • DOI: 10.1186/s40168-018-0580-7

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces
journal, April 2019

  • Checinska Sielaff, Aleksandra; Urbaniak, Camilla; Mohan, Ganesh Babu Malli
  • Microbiome, Vol. 7, Issue 1
  • DOI: 10.1186/s40168-019-0666-x

Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance
journal, January 2020


Microbial communities from arid environments on a global scale. A systematic review
journal, July 2020


Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements
journal, November 2019

  • Snelling, Timothy J.; Auffret, Marc D.; Duthie, Carol-Anne
  • Animal Microbiome, Vol. 1, Issue 1
  • DOI: 10.1186/s42523-019-0018-y

A census-based estimate of Earth's bacterial and archaeal diversity
journal, February 2019


High-order interactions distort the functional landscape of microbial consortia
journal, December 2019


Latent environment allocation of microbial community data
journal, June 2018


Erythritol as a single carbon source improves cultural isolation of Burkholderia pseudomallei from rice paddy soils
journal, October 2019


The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities
journal, January 2019

  • Rocca, Jennifer D.; Simonin, Marie; Blaszczak, Joanna R.
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.03272

Microbial Community Analysis of Sauerkraut Fermentation Reveals a Stable and Rapidly Established Community
journal, May 2018


Coupled Biological and Abiotic Mechanisms Driving Carbonyl Sulfide Production in Soils
journal, June 2018


Comparison of extraction methods for recovering ancient microbial DNA from paleofeces
journal, November 2019

  • Hagan, Richard W.; Hofman, Courtney A.; Hübner, Alexander
  • American Journal of Physical Anthropology, Vol. 171, Issue 2
  • DOI: 10.1002/ajpa.23978

Think global, act local: The small‐scale environment mainly influences microbial community development and function in lake sediment
journal, January 2020

  • Orland, Chloé; Yakimovich, Kurt M.; Mykytczuk, Nadia C. S.
  • Limnology and Oceanography, Vol. 65, Issue S1
  • DOI: 10.1002/lno.11370

Linking metagenomics to aquatic microbial ecology and biogeochemical cycles
journal, January 2020

  • Grossart, Hans‐Peter; Massana, Ramon; McMahon, Katherine D.
  • Limnology and Oceanography, Vol. 65, Issue S1
  • DOI: 10.1002/lno.11382

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea
journal, August 2018

  • Albright, Michaeline B. N.; Timalsina, Bibek; Martiny, Jennifer B. H.
  • Microbial Ecology, Vol. 77, Issue 3
  • DOI: 10.1007/s00248-018-1239-4

Microbial assemblages and bioindicators as proxies for ecosystem health status: potential and limitations
journal, June 2019

  • Astudillo-García, Carmen; Hermans, Syrie M.; Stevenson, Bryan
  • Applied Microbiology and Biotechnology, Vol. 103, Issue 16
  • DOI: 10.1007/s00253-019-09963-0

Clinician Guide to Microbiome Testing
journal, September 2018

  • Staley, Christopher; Kaiser, Thomas; Khoruts, Alexander
  • Digestive Diseases and Sciences, Vol. 63, Issue 12
  • DOI: 10.1007/s10620-018-5299-6

Evolutionary constraints on species diversity in marine bacterioplankton communities
journal, January 2019


Dispersal homogenizes communities via immigration even at low rates in a simplified synthetic bacterial metacommunity
journal, March 2019

  • Fodelianakis, Stilianos; Lorz, Alexander; Valenzuela-Cuevas, Adriana
  • Nature Communications, Vol. 10, Issue 1
  • DOI: 10.1038/s41467-019-09306-7

Uncovering the biosynthetic potential of rare metagenomic DNA using co-occurrence network analysis of targeted sequences
journal, August 2019


Global diversity and biogeography of bacterial communities in wastewater treatment plants
journal, May 2019


FEAST: fast expectation-maximization for microbial source tracking
journal, June 2019


Differences in the fecal microbiota of neonates born at home or in the hospital
journal, October 2018


Uncovering the hidden marine sponge microbiome by applying a multi-primer approach
journal, April 2019


Current challenges and best-practice protocols for microbiome analysis
journal, December 2019


Characterization of the microbiome and bioluminescent symbionts across life stages of Ceratioid Anglerfishes of the Gulf of Mexico
journal, September 2019

  • Freed, Lindsay L.; Easson, Cole; Baker, Lydia J.
  • FEMS Microbiology Ecology, Vol. 95, Issue 10
  • DOI: 10.1093/femsec/fiz146

Bacterial–fungal interactions: ecology, mechanisms and challenges
journal, February 2018

  • Deveau, Aurélie; Bonito, Gregory; Uehling, Jessie
  • FEMS Microbiology Reviews, Vol. 42, Issue 3
  • DOI: 10.1093/femsre/fuy008

From hairballs to hypotheses–biological insights from microbial networks
journal, July 2018

  • Röttjers, Lisa; Faust, Karoline
  • FEMS Microbiology Reviews, Vol. 42, Issue 6
  • DOI: 10.1093/femsre/fuy030

Systematic processing of ribosomal RNA gene amplicon sequencing data
journal, December 2019


Mechanisms of soil bacterial and fungal community assembly differ among and within islands
journal, December 2019


Interactome‐based abiotic and biotic impacts on biodiversity of plankton communities in disturbed wetlands
journal, June 2019

  • Yang, Yuzhan; Gao, Yangchun; Chen, Yiyong
  • Diversity and Distributions, Vol. 25, Issue 9
  • DOI: 10.1111/ddi.12949

Latitudinal variation in soil nematode communities under climate warming‐related range‐expanding and native plants
journal, May 2019

  • Wilschut, Rutger A.; Geisen, Stefan; Martens, Henk
  • Global Change Biology, Vol. 25, Issue 8
  • DOI: 10.1111/gcb.14657

Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis
journal, January 2018

  • Porter, Teresita M.; Hajibabaei, Mehrdad
  • Molecular Ecology, Vol. 27, Issue 2
  • DOI: 10.1111/mec.14478

Introduction: The host-associated microbiome: Pattern, process and function
journal, April 2018

  • Parfrey, Laura Wegener; Moreau, Corrie S.; Russell, Jacob A.
  • Molecular Ecology, Vol. 27, Issue 8
  • DOI: 10.1111/mec.14706

Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges
journal, November 2019

  • Zhou, Kun; Zhang, Rui; Sun, Jin
  • Applied and Environmental Microbiology, Vol. 85, Issue 22
  • DOI: 10.1128/AEM.00992-19

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
journal, February 2018

  • Pollock, Jolinda; Glendinning, Laura; Wisedchanwet, Trong
  • Applied and Environmental Microbiology, Vol. 84, Issue 7
  • DOI: 10.1128/aem.02627-17

Use of a Fluorescent Analog of Glucose (2-NBDG) To Identify Uncultured Rumen Bacteria That Take Up Glucose
journal, February 2019

  • Tao, Junyi; McCourt, Courtney; Sultana, Halima
  • Applied and Environmental Microbiology, Vol. 85, Issue 7
  • DOI: 10.1128/aem.03018-18

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations
journal, June 2019


The power of crowds: Grand challenges in the Asia-Pacific region
journal, September 2019

  • Cai, Cynthia Weiyi; Gippel, Jennifer; Zhu, Yushu
  • Australian Journal of Management, Vol. 44, Issue 4
  • DOI: 10.1177/0312896219871979

EMPeror: a tool for visualizing high-throughput microbial community data
journal, November 2013

  • Vázquez-Baeza, Yoshiki; Pirrung, Meg; Gonzalez, Antonio
  • GigaScience, Vol. 2, Issue 1
  • DOI: 10.1186/2047-217X-2-16

Charting the diversity of uncultured viruses of Archaea and Bacteria
journal, December 2019


Expanding the scope and scale of microbiome research
journal, September 2019


Challenges in the construction of knowledge bases for human microbiome-disease associations
journal, September 2019


A conceptual framework for the phylogenetically constrained assembly of microbial communities
journal, October 2019


Chemical and microbial diversity covary in fresh water to influence ecosystem functioning
text, January 2019

  • Tanentzap, Andrew; Fitch, Amelia; Orland, Chloe
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45125

Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment
journal, February 2019

  • Warren-Rhodes, Kimberley A.; Lee, Kevin C.; Archer, Stephen D. J.
  • Frontiers in Microbiology, Vol. 10
  • DOI: 10.3389/fmicb.2019.00069

Does Soil Contribute to the Human Gut Microbiome?
journal, August 2019

  • Blum, Winfried E. H.; Zechmeister-Boltenstern, Sophie; Keiblinger, Katharina M.
  • Microorganisms, Vol. 7, Issue 9
  • DOI: 10.3390/microorganisms7090287

A hierarchy of environmental covariates control the global biogeography of soil bacterial richness
text, January 2019


Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
text, January 2019


Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate
text, January 2020

  • Wang, Yun; Kapun, Martin; Waidele, Lena
  • Wiley-Blackwell Publishing, Inc.
  • DOI: 10.5167/uzh-195892

The effect of captivity on the primate gut microbiome varies with host dietary niche
journal, November 2019

  • Frankel, Jeffrey S.; Mallott, Elizabeth K.; Hopper, Lydia M.
  • American Journal of Primatology, Vol. 81, Issue 12
  • DOI: 10.1002/ajp.23061

Response and driving factors of soil microbial diversity related to global nitrogen addition
journal, October 2019

  • Yang, Yang; Cheng, Huan; Gao, Han
  • Land Degradation & Development, Vol. 31, Issue 2
  • DOI: 10.1002/ldr.3439

Cross-Biome Drivers of Soil Bacterial Alpha Diversity on a Worldwide Scale
journal, January 2019


Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy
journal, June 2019

  • Weissman, Jake L.; Laljani, Rohan M. R.; Fagan, William F.
  • The ISME Journal, Vol. 13, Issue 10
  • DOI: 10.1038/s41396-019-0411-2

Home chemical and microbial transitions across urbanization
journal, November 2019


The hunt for the most-wanted chemolithoautotrophic spookmicrobes
journal, April 2018

  • in ‘t Zandt, Michiel H.; de Jong, Anniek EE; Slomp, Caroline P.
  • FEMS Microbiology Ecology, Vol. 94, Issue 6
  • DOI: 10.1093/femsec/fiy064

Taxonomic classification method for metagenomics based on core protein families with Core-Kaiju
journal, July 2020

  • Tovo, Anna; Menzel, Peter; Krogh, Anders
  • Nucleic Acids Research, Vol. 48, Issue 16
  • DOI: 10.1093/nar/gkaa568

MGnify: the microbiome analysis resource in 2020
journal, November 2019

  • Mitchell, Alex L.; Almeida, Alexandre; Beracochea, Martin
  • Nucleic Acids Research
  • DOI: 10.1093/nar/gkz1035

Contrasting patterns of plant and microbial diversity during long-term ecosystem development
journal, January 2019

  • Turner, Benjamin L.; Zemunik, Graham; Laliberté, Etienne
  • Journal of Ecology, Vol. 107, Issue 2
  • DOI: 10.1111/1365-2745.13127

Latent Dirichlet Allocation reveals spatial and taxonomic structure in a DNA‐based census of soil biodiversity from a tropical forest
journal, December 2019

  • Sommeria‐Klein, Guilhem; Zinger, Lucie; Coissac, Eric
  • Molecular Ecology Resources, Vol. 20, Issue 2
  • DOI: 10.1111/1755-0998.13109

Towards a systematic understanding of differences between archaeal and bacterial diversity: Systematic understanding of differences
journal, November 2018


Host genetic determinants of the gut microbiota of wild mice
journal, June 2019

  • Suzuki, Taichi A.; Phifer‐Rixey, Megan; Mack, Katya L.
  • Molecular Ecology, Vol. 28, Issue 13
  • DOI: 10.1111/mec.15139

The relative importance of ecological drivers of arbuscular mycorrhizal fungal distribution varies with taxon phylogenetic resolution
journal, September 2019

  • Roy, Julien; Mazel, Florent; Sosa‐Hernández, Moisés A.
  • New Phytologist, Vol. 224, Issue 2
  • DOI: 10.1111/nph.16080

Inferring macro‐ecological patterns from local presence/absence data
journal, August 2019

  • Tovo, Anna; Formentin, Marco; Suweis, Samir
  • Oikos, Vol. 128, Issue 11
  • DOI: 10.1111/oik.06754

Metagenome Sequences of Sediment from a Recovering Industrialized Appalachian River in West Virginia
journal, May 2018

  • Huber, David H.; Ugwuanyi, Ifeoma R.; Malkaram, Sridhar A.
  • Genome Announcements, Vol. 6, Issue 18
  • DOI: 10.1128/genomea.00350-18

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats
journal, January 2020


Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
journal, April 2018


American Gut: an Open Platform for Citizen Science Microbiome Research
journal, May 2018


Selection, Succession, and Stabilization of Soil Microbial Consortia
journal, May 2019


Metagenomic Approaches for Understanding New Concepts in Microbial Science
journal, August 2018

  • Alves, Luana de Fátima; Westmann, Cauã Antunes; Lovate, Gabriel Lencioni
  • International Journal of Genomics, Vol. 2018
  • DOI: 10.1155/2018/2312987

Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions
journal, January 2019

  • Christoff, Ana P.; Sereia, Aline FR; Hernandes, Camila
  • Experimental Biology and Medicine, Vol. 244, Issue 6
  • DOI: 10.1177/1535370218821857

Synergistic effects of APOE and sex on the gut microbiome of young EFAD transgenic mice
journal, December 2019

  • Maldonado Weng, Juan; Parikh, Ishita; Naqib, Ankur
  • Molecular Neurodegeneration, Vol. 14, Issue 1
  • DOI: 10.1186/s13024-019-0352-2

Parasite microbiome project: Grand challenges
journal, October 2019


Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition
journal, June 2018


Global Observational Needs and Resources for Marine Biodiversity
journal, July 2019

  • Canonico, Gabrielle; Buttigieg, Pier Luigi; Montes, Enrique
  • Frontiers in Marine Science, Vol. 6
  • DOI: 10.3389/fmars.2019.00367

A Response to Scientific and Societal Needs for Marine Biological Observations
journal, July 2019

  • Bax, Nicholas J.; Miloslavich, Patricia; Muller-Karger, Frank Edgar
  • Frontiers in Marine Science, Vol. 6
  • DOI: 10.3389/fmars.2019.00395

Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function
journal, August 2018

  • Ghuneim, Lydia-Ann J.; Jones, David L.; Golyshin, Peter N.
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.01971

Optimal Microbiome Networks: Macroecology and Criticality
journal, May 2019


Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling
journal, June 2019

  • Rampelotto, Pabulo H.; Sereia, Aline F. R.; de Oliveira, Luiz Felipe V.
  • International Journal of Molecular Sciences, Vol. 20, Issue 12
  • DOI: 10.3390/ijms20123099

Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis
journal, October 2018

  • Maricic, Igor; Marrero, Idania; Eguchi, Akiko
  • The Journal of Immunology, Vol. 201, Issue 10
  • DOI: 10.4049/jimmunol.1800614

Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework
text, January 2019

  • Wasimuddin, Wasimuddin; Schlaeppi, Klaus; Ronchi, Francesca
  • Cold Spring Harbor Laboratory
  • DOI: 10.7892/boris.135376

The gut microbiome of nonhuman primates: Lessons in ecology and evolution
journal, June 2018

  • Clayton, Jonathan B.; Gomez, Andres; Amato, Katherine
  • American Journal of Primatology, Vol. 80, Issue 6
  • DOI: 10.1002/ajp.22867

Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity
journal, July 2018


Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome
journal, January 2020


Community-level signatures of ecological succession in natural bacterial communities
journal, May 2020


Polarization of microbial communities between competitive and cooperative metabolism
journal, January 2021

  • Machado, Daniel; Maistrenko, Oleksandr M.; Andrejev, Sergej
  • Nature Ecology & Evolution, Vol. 5, Issue 2
  • DOI: 10.1038/s41559-020-01353-4

Soil microbiomes and climate change
journal, October 2019


Marchantia liverworts as a proxy to plants’ basal microbiomes
journal, August 2018


The known and the unknown in soil microbial ecology
journal, January 2019


Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis
journal, March 2019

  • Helber, Stephanie B.; Steinert, Georg; Wu, Yu-Chen
  • FEMS Microbiology Ecology, Vol. 95, Issue 4
  • DOI: 10.1093/femsec/fiz026

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
journal, May 2018


gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data
journal, October 2018

  • Shi, Wenyu; Qi, Heyuan; Sun, Qinglan
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1008

Conserving the holobiont
journal, April 2020

  • Carthey, Alexandra J. R.; Blumstein, Daniel T.; Gallagher, Rachael V.
  • Functional Ecology, Vol. 34, Issue 4
  • DOI: 10.1111/1365-2435.13504

Microbial diversity and biogeography in Arctic soils: Microbial diversity and biogeography
journal, August 2018

  • Malard, Lucie A.; Pearce, David A.
  • Environmental Microbiology Reports, Vol. 10, Issue 6
  • DOI: 10.1111/1758-2229.12680

Impacts of indoor surface finishes on bacterial viability
journal, May 2019

  • Hu, Jinglin; Ben Maamar, Sarah; Glawe, Adam J.
  • Indoor Air, Vol. 29, Issue 4
  • DOI: 10.1111/ina.12558

Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study
journal, August 2019

  • Saborío‐Montero, Alejandro; Gutiérrez‐Rivas, Mónica; García‐Rodríguez, Aser
  • Journal of Animal Breeding and Genetics, Vol. 137, Issue 1
  • DOI: 10.1111/jbg.12444

DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions
journal, April 2019

  • Zinger, Lucie; Bonin, Aurélie; Alsos, Inger G.
  • Molecular Ecology, Vol. 28, Issue 8
  • DOI: 10.1111/mec.15060

Identifying and Predicting Novelty in Microbiome Studies
journal, December 2018


Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease
journal, February 2019


Protein tyrosine phosphatase non-receptor type 22 modulates colitis in a microbiota-dependent manner
journal, April 2019

  • Spalinger, Marianne R.; Schmidt, Thomas S. B.; Schwarzfischer, Marlene
  • Journal of Clinical Investigation, Vol. 129, Issue 6
  • DOI: 10.1172/jci123263

High-throughput DNA sequencing technologies for water and wastewater analysis
journal, October 2019

  • Chan, Alexander WY; Naphtali, James; Schellhorn, Herb E.
  • Science Progress, Vol. 102, Issue 4
  • DOI: 10.1177/0036850419881855

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus
journal, November 2018


Coexistence and cooperation in structured habitats
journal, March 2020


A global survey of arsenic-related genes in soil microbiomes
journal, May 2019


CAMISIM: simulating metagenomes and microbial communities
journal, February 2019


Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities
journal, February 2019


The Microbial Landscape of Sea Stars and the Anatomical and Interspecies Variability of Their Microbiome
journal, August 2018

  • Jackson, Elliot W.; Pepe-Ranney, Charles; Debenport, Spencer J.
  • Frontiers in Microbiology, Vol. 9
  • DOI: 10.3389/fmicb.2018.01829

Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands
journal, January 2019

  • Warwick-Dugdale, Joanna; Solonenko, Natalie; Moore, Karen
  • PeerJ, Vol. 7
  • DOI: 10.7717/peerj.6800

Species abundance information improves sequence taxonomy classification accuracy
journal, October 2019

  • Kaehler, Benjamin D.; Bokulich, Nicholas A.; McDonald, Daniel
  • Nature Communications, Vol. 10, Issue 1
  • DOI: 10.1038/s41467-019-12669-6

A meta-analysis of global fungal distribution reveals climate-driven patterns
journal, November 2019


Insect herbivory reshapes a native leaf microbiome
journal, January 2020


Airborne microbial transport limitation to isolated Antarctic soil habitats
journal, March 2019


Global change microbiology — big questions about small life for our future
journal, May 2019


Soil nematode abundance and functional group composition at a global scale
journal, July 2019


phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
journal, October 2019


Dormancy dynamics and dispersal contribute to soil microbiome resilience
journal, March 2020

  • Sorensen, Jackson W.; Shade, Ashley
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 375, Issue 1798
  • DOI: 10.1098/rstb.2019.0255

Elucidating the ecological networks in stone‐dwelling microbiomes
journal, April 2020

  • Louati, Moussa; Ennis, Nathaniel J.; Ghodhbane‐Gtari, Faten
  • Environmental Microbiology, Vol. 22, Issue 4
  • DOI: 10.1111/1462-2920.14700

Interdomain ecological networks between plants and microbes
journal, September 2019


Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate
journal, February 2020

  • Wang, Yun; Kapun, Martin; Waidele, Lena
  • Environmental Microbiology Reports, Vol. 12, Issue 2
  • DOI: 10.1111/1758-2229.12826

Biogeography of soil bacteria and archaea across France
journal, July 2018

  • Karimi, Battle; Terrat, Sébastien; Dequiedt, Samuel
  • Science Advances, Vol. 4, Issue 7
  • DOI: 10.1126/sciadv.aat1808

Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria
journal, January 2020

  • Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W.
  • mBio, Vol. 11, Issue 1
  • DOI: 10.1128/mbio.02293-19

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
journal, January 2020


Microbiome of vineyard soils is shaped by geography and management
journal, November 2019


Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities
journal, November 2019


Microbial Diversity Exploration of Marine Hosts at Serrana Bank, a Coral Atoll of the Seaflower Biosphere Reserve
journal, June 2019

  • Alvarez-Yela, Astrid Catalina; Mosquera-Rendón, Jeanneth; Noreña-P, Alejandra
  • Frontiers in Marine Science, Vol. 6
  • DOI: 10.3389/fmars.2019.00338

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models
journal, February 2018

  • Belk, Aeriel; Xu, Zhenjiang Zech; Carter, David O.
  • Genes, Vol. 9, Issue 2
  • DOI: 10.3390/genes9020104

Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents
journal, January 2019


Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage
journal, August 2019


Streaming histogram sketching for rapid microbiome analytics
journal, March 2019


Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
journal, January 2020


The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics
journal, January 2018


Latitudinal gradient of cyanobacterial diversity in tidal flats
journal, November 2019


Host-mediated microbiome engineering (HMME) of drought tolerance in the wheat rhizosphere
journal, December 2019


The Community Simulator: A Python package for microbial ecology
journal, March 2020


The Role of Soil Fungi in K+ Plant Nutrition
journal, June 2019

  • Haro, Rosario; Benito, Begoña
  • International Journal of Molecular Sciences, Vol. 20, Issue 13
  • DOI: 10.3390/ijms20133169

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota
journal, January 2020

  • García-López, Rodrigo; Cornejo-Granados, Fernanda; Lopez-Zavala, Alonso A.
  • Microorganisms, Vol. 8, Issue 1
  • DOI: 10.3390/microorganisms8010134