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1. A longitudinal big data approach for precision health.

Author: Schüssler-Fiorenza Rose, Sophia Miryam, Schüssler-Fiorenza Rose, Sophia Miryam, Contrepois, Kévin, Moneghetti, Kegan J, Zhou, Wenyu, Mishra, Tejaswini, Mataraso, Samson, Dagan-Rosenfeld, Orit, Ganz, Ariel B, Dunn, Jessilyn, Hornburg, Daniel, Rego, Shannon, Perelman, Dalia, Ahadi, Sara, Sailani, M Reza, Zhou, Yanjiao, Leopold, Shana R, Chen, Jieming, Ashland, Melanie, Christle, Jeffrey W, Avina, Monika, Limcaoco, Patricia, Ruiz, Camilo, Tan, Marilyn, Butte, Atul J, Weinstock, George M, Slavich, George M, Sodergren, Erica, McLaughlin, Tracey L, Haddad, Francois, Snyder, Michael P, Schüssler-Fiorenza Rose, Sophia Miryam, Schüssler-Fiorenza Rose, Sophia Miryam, Contrepois, Kévin, Moneghetti, Kegan J, Zhou, Wenyu, Mishra, Tejaswini, Mataraso, Samson, Dagan-Rosenfeld, Orit, Ganz, Ariel B, Dunn, Jessilyn, Hornburg, Daniel, Rego, Shannon, Perelman, Dalia, Ahadi, Sara, Sailani, M Reza, Zhou, Yanjiao, Leopold, Shana R, Chen, Jieming, Ashland, Melanie, Christle, Jeffrey W, Avina, Monika, Limcaoco, Patricia, Ruiz, Camilo, Tan, Marilyn, Butte, Atul J, Weinstock, George M, Slavich, George M, Sodergren, Erica, McLaughlin, Tracey L, Haddad, Francois, and Snyder, Michael P
Abstract: Precision health relies on the ability to assess disease risk at an individual level, detect early preclinical conditions and initiate preventive strategies. Recent technological advances in omics and wearable monitoring enable deep molecular and physiological profiling and may provide important tools for precision health. We explored the ability of deep longitudinal profiling to make health-related discoveries, identify clinically relevant molecular pathways and affect behavior in a prospective longitudinal cohort (n = 109) enriched for risk of type 2 diabetes mellitus. The cohort underwent integrative personalized omics profiling from samples collected quarterly for up to 8 years (median, 2.8 years) using clinical measures and emerging technologies including genome, immunome, transcriptome, proteome, metabolome, microbiome and wearable monitoring. We discovered more than 67 clinically actionable health discoveries and identified multiple molecular pathways associated with metabolic, cardiovascular and oncologic pathophysiology. We developed prediction models for insulin resistance by using omics measurements, illustrating their potential to replace burdensome tests. Finally, study participation led the majority of participants to implement diet and exercise changes. Altogether, we conclude that deep longitudinal profiling can lead to actionable health discoveries and provide relevant information for precision health.
Published: 2019

2. Toward unrestricted use of public genomic data.

Author: Amann, Rudolf I, Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, Xenarios, Ioannis, Amann, Rudolf I, Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, and Xenarios, Ioannis
Published: 2019

3. Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Author: Zhou, Wenyu, Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, Snyder, Michael, Zhou, Wenyu, Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, and Snyder, Michael
Abstract: Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.
Published: 2019

4. Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Author: Zhou, Wenyu, Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, Snyder, Michael, Zhou, Wenyu, Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, and Snyder, Michael
Abstract: Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.
Published: 2019

5. Consent insufficient for data release−Response

Author: Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., Xenarios, Ioannis, Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis
Published: 2019

6. Data access: Toward unrestricted use of public genomic data

Author: Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, De Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., Xenarios, Ioannis, Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, De Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis
Published: 2019

7. Toward unrestricted use of public genomic data.

Author: Amann, Rudolf I, Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, Xenarios, Ioannis, Amann, Rudolf I, Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, and Xenarios, Ioannis
Abstract: Publication interests should not limit access to public data
Published: 2019

8. A longitudinal big data approach for precision health.

Author: Schüssler-Fiorenza Rose, Sophia Miryam, Schüssler-Fiorenza Rose, Sophia Miryam, Contrepois, Kévin, Moneghetti, Kegan J, Zhou, Wenyu, Mishra, Tejaswini, Mataraso, Samson, Dagan-Rosenfeld, Orit, Ganz, Ariel B, Dunn, Jessilyn, Hornburg, Daniel, Rego, Shannon, Perelman, Dalia, Ahadi, Sara, Sailani, M Reza, Zhou, Yanjiao, Leopold, Shana R, Chen, Jieming, Ashland, Melanie, Christle, Jeffrey W, Avina, Monika, Limcaoco, Patricia, Ruiz, Camilo, Tan, Marilyn, Butte, Atul J, Weinstock, George M, Slavich, George M, Sodergren, Erica, McLaughlin, Tracey L, Haddad, Francois, Snyder, Michael P, Schüssler-Fiorenza Rose, Sophia Miryam, Schüssler-Fiorenza Rose, Sophia Miryam, Contrepois, Kévin, Moneghetti, Kegan J, Zhou, Wenyu, Mishra, Tejaswini, Mataraso, Samson, Dagan-Rosenfeld, Orit, Ganz, Ariel B, Dunn, Jessilyn, Hornburg, Daniel, Rego, Shannon, Perelman, Dalia, Ahadi, Sara, Sailani, M Reza, Zhou, Yanjiao, Leopold, Shana R, Chen, Jieming, Ashland, Melanie, Christle, Jeffrey W, Avina, Monika, Limcaoco, Patricia, Ruiz, Camilo, Tan, Marilyn, Butte, Atul J, Weinstock, George M, Slavich, George M, Sodergren, Erica, McLaughlin, Tracey L, Haddad, Francois, and Snyder, Michael P
Abstract: Precision health relies on the ability to assess disease risk at an individual level, detect early preclinical conditions and initiate preventive strategies. Recent technological advances in omics and wearable monitoring enable deep molecular and physiological profiling and may provide important tools for precision health. We explored the ability of deep longitudinal profiling to make health-related discoveries, identify clinically relevant molecular pathways and affect behavior in a prospective longitudinal cohort (n = 109) enriched for risk of type 2 diabetes mellitus. The cohort underwent integrative personalized omics profiling from samples collected quarterly for up to 8 years (median, 2.8 years) using clinical measures and emerging technologies including genome, immunome, transcriptome, proteome, metabolome, microbiome and wearable monitoring. We discovered more than 67 clinically actionable health discoveries and identified multiple molecular pathways associated with metabolic, cardiovascular and oncologic pathophysiology. We developed prediction models for insulin resistance by using omics measurements, illustrating their potential to replace burdensome tests. Finally, study participation led the majority of participants to implement diet and exercise changes. Altogether, we conclude that deep longitudinal profiling can lead to actionable health discoveries and provide relevant information for precision health.
Published: 2019

9. Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Author: Zhou, Wenyu, Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, Snyder, Michael, Zhou, Wenyu, Zhou, Wenyu, Sailani, M Reza, Contrepois, Kévin, Zhou, Yanjiao, Ahadi, Sara, Leopold, Shana R, Zhang, Martin J, Rao, Varsha, Avina, Monika, Mishra, Tejaswini, Johnson, Jethro, Lee-McMullen, Brittany, Chen, Songjie, Metwally, Ahmed A, Tran, Thi Dong Binh, Nguyen, Hoan, Zhou, Xin, Albright, Brandon, Hong, Bo-Young, Petersen, Lauren, Bautista, Eddy, Hanson, Blake, Chen, Lei, Spakowicz, Daniel, Bahmani, Amir, Salins, Denis, Leopold, Benjamin, Ashland, Melanie, Dagan-Rosenfeld, Orit, Rego, Shannon, Limcaoco, Patricia, Colbert, Elizabeth, Allister, Candice, Perelman, Dalia, Craig, Colleen, Wei, Eric, Chaib, Hassan, Hornburg, Daniel, Dunn, Jessilyn, Liang, Liang, Rose, Sophia Miryam Schüssler-Fiorenza, Kukurba, Kim, Piening, Brian, Rost, Hannes, Tse, David, McLaughlin, Tracey, Sodergren, Erica, Weinstock, George M, and Snyder, Michael
Abstract: Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.
Published: 2019

10. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss

Author: Piening, Brian D., Zhou, Wenyu, Contrepois, Kévin, Röst, Hannes, Gu Urban, Gucci Jijuan, Mishra, Tejaswini, Hanson, Blake M., Bautista, Eddy J., Leopold, Shana, Yeh, Christine Y., Spakowicz, Daniel, Banerjee, Imon, Chen, Cynthia, Kukurba, Kimberly, Perelman, Dalia, Craig, Colleen, Colbert, Elizabeth, Salins, Denis, Rego, Shannon, Lee, Sunjae, Zhang, Cheng, Wheeler, Jessica, Sailani, M. Reza, Liang, Liang, Abbott, Charles, Gerstein, Mark, Mardinoglu, Adil, Smith, Ulf, Rubin, Daniel L., Pitteri, Sharon, Sodergren, Erica, McLaughlin, Tracey L., Weinstock, George M., Snyder, Michael P., Piening, Brian D., Zhou, Wenyu, Contrepois, Kévin, Röst, Hannes, Gu Urban, Gucci Jijuan, Mishra, Tejaswini, Hanson, Blake M., Bautista, Eddy J., Leopold, Shana, Yeh, Christine Y., Spakowicz, Daniel, Banerjee, Imon, Chen, Cynthia, Kukurba, Kimberly, Perelman, Dalia, Craig, Colleen, Colbert, Elizabeth, Salins, Denis, Rego, Shannon, Lee, Sunjae, Zhang, Cheng, Wheeler, Jessica, Sailani, M. Reza, Liang, Liang, Abbott, Charles, Gerstein, Mark, Mardinoglu, Adil, Smith, Ulf, Rubin, Daniel L., Pitteri, Sharon, Sodergren, Erica, McLaughlin, Tracey L., Weinstock, George M., and Snyder, Michael P.
Abstract: Advances in omics technologies now allow an unprecedented level of phenotyping for human diseases, including obesity, in which individual responses to excess weight are heterogeneous and unpredictable. To aid the development of better understanding of these phenotypes, we performed a controlled longitudinal weight perturbation study combining multiple omics strategies (genomics, transcriptomics, multiple proteomics assays, metabolomics, and microbiomics) during periods of weight gain and loss in humans. Results demonstrated that: (1) weight gain is associated with the activation of strong inflammatory and hypertrophic cardiomyopathy signatures in blood; (2) although weight loss reverses some changes, a number of signatures persist, indicative of long-term physiologic changes; (3) we observed omics signatures associated with insulin resistance that may serve as novel diagnostics; (4) specific biomolecules were highly individualized and stable in response to perturbations, potentially representing stable personalized markers. Most data are available open access and serve as a valuable resource for the community.
Published: 2018
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11. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author: Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Published: 2018

12. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author: Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Abstract: In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.
Published: 2018

13. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)

Author: Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, other, and, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, and other, and
Abstract: In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.
Published: 2018

14. Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., Bowers, Robert M., Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., and Bowers, Robert M.
Abstract: Nat. Biotechnol. 35, 725–731 (2017); published online 8 August 2017; corrected after print 29 November 2017; corrected after print 7 December 2017 In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.
Published: 2018

15. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author: Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Published: 2018

16. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author: Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Abstract: In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.
Published: 2018

17. Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Published: 2018

18. Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, A Murat, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Published: 2018

19. Enterotypes in the landscape of gut microbial community composition.

Author: Costea, Paul I, Costea, Paul I, Hildebrand, Falk, Arumugam, Manimozhiyan, Bäckhed, Fredrik, Blaser, Martin J, Bushman, Frederic D, de Vos, Willem M, Ehrlich, S Dusko, Fraser, Claire M, Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B, Knights, Dan, Lewis, James D, Ley, Ruth E, Ochman, Howard, O'Toole, Paul W, Quince, Christopher, Relman, David A, Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M, Wu, Gary D, Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, Bork, Peer, Costea, Paul I, Costea, Paul I, Hildebrand, Falk, Arumugam, Manimozhiyan, Bäckhed, Fredrik, Blaser, Martin J, Bushman, Frederic D, de Vos, Willem M, Ehrlich, S Dusko, Fraser, Claire M, Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B, Knights, Dan, Lewis, James D, Ley, Ruth E, Ochman, Howard, O'Toole, Paul W, Quince, Christopher, Relman, David A, Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M, Wu, Gary D, Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, and Bork, Peer
Abstract: Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
Published: 2018

20. Enterotypes in the landscape of gut microbial community composition

Author: Costea, Paul I., Hildebrand, Falk, Manimozhiyan, Arumugam, Bäckhed, Fredrik, Blaser, Martin J., Bushman, Frederic D., De Vos, Willem M., Ehrlich, S. Dusko, Fraser, Claire M., Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B., Knights, Dan, Lewis, James D., Ley, Ruth E., Ochman, Howard, O'Toole, Paul W., Quince, Christopher, Relman, David A., Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M., Wu, Gary D., Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, Bork, Peer, Costea, Paul I., Hildebrand, Falk, Manimozhiyan, Arumugam, Bäckhed, Fredrik, Blaser, Martin J., Bushman, Frederic D., De Vos, Willem M., Ehrlich, S. Dusko, Fraser, Claire M., Hattori, Masahira, Huttenhower, Curtis, Jeffery, Ian B., Knights, Dan, Lewis, James D., Ley, Ruth E., Ochman, Howard, O'Toole, Paul W., Quince, Christopher, Relman, David A., Shanahan, Fergus, Sunagawa, Shinichi, Wang, Jun, Weinstock, George M., Wu, Gary D., Zeller, Georg, Zhao, Liping, Raes, Jeroen, Knight, Rob, and Bork, Peer
Abstract: Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.
Published: 2018

21. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017
Full Text: View/download PDF

22. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017
Full Text: View/download PDF

23. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017
Full Text: View/download PDF

24. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author: Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017

25. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

Author: Jasinska, Anna J, Jasinska, Anna J, Zelaya, Ivette, Service, Susan K, Peterson, Christine B, Cantor, Rita M, Choi, Oi-Wa, DeYoung, Joseph, Eskin, Eleazar, Fairbanks, Lynn A, Fears, Scott, Furterer, Allison E, Huang, Yu S, Ramensky, Vasily, Schmitt, Christopher A, Svardal, Hannes, Jorgensen, Matthew J, Kaplan, Jay R, Villar, Diego, Aken, Bronwen L, Flicek, Paul, Nag, Rishi, Wong, Emily S, Blangero, John, Dyer, Thomas D, Bogomolov, Marina, Benjamini, Yoav, Weinstock, George M, Dewar, Ken, Sabatti, Chiara, Wilson, Richard K, Jentsch, J David, Warren, Wesley, Coppola, Giovanni, Woods, Roger P, Freimer, Nelson B, Jasinska, Anna J, Jasinska, Anna J, Zelaya, Ivette, Service, Susan K, Peterson, Christine B, Cantor, Rita M, Choi, Oi-Wa, DeYoung, Joseph, Eskin, Eleazar, Fairbanks, Lynn A, Fears, Scott, Furterer, Allison E, Huang, Yu S, Ramensky, Vasily, Schmitt, Christopher A, Svardal, Hannes, Jorgensen, Matthew J, Kaplan, Jay R, Villar, Diego, Aken, Bronwen L, Flicek, Paul, Nag, Rishi, Wong, Emily S, Blangero, John, Dyer, Thomas D, Bogomolov, Marina, Benjamini, Yoav, Weinstock, George M, Dewar, Ken, Sabatti, Chiara, Wilson, Richard K, Jentsch, J David, Warren, Wesley, Coppola, Giovanni, Woods, Roger P, and Freimer, Nelson B
Abstract: By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.
Published: 2017

26. Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate.

Author: Jasinska, Anna J, Jasinska, Anna J, Zelaya, Ivette, Service, Susan K, Peterson, Christine B, Cantor, Rita M, Choi, Oi-Wa, DeYoung, Joseph, Eskin, Eleazar, Fairbanks, Lynn A, Fears, Scott, Furterer, Allison E, Huang, Yu S, Ramensky, Vasily, Schmitt, Christopher A, Svardal, Hannes, Jorgensen, Matthew J, Kaplan, Jay R, Villar, Diego, Aken, Bronwen L, Flicek, Paul, Nag, Rishi, Wong, Emily S, Blangero, John, Dyer, Thomas D, Bogomolov, Marina, Benjamini, Yoav, Weinstock, George M, Dewar, Ken, Sabatti, Chiara, Wilson, Richard K, Jentsch, J David, Warren, Wesley, Coppola, Giovanni, Woods, Roger P, Freimer, Nelson B, Jasinska, Anna J, Jasinska, Anna J, Zelaya, Ivette, Service, Susan K, Peterson, Christine B, Cantor, Rita M, Choi, Oi-Wa, DeYoung, Joseph, Eskin, Eleazar, Fairbanks, Lynn A, Fears, Scott, Furterer, Allison E, Huang, Yu S, Ramensky, Vasily, Schmitt, Christopher A, Svardal, Hannes, Jorgensen, Matthew J, Kaplan, Jay R, Villar, Diego, Aken, Bronwen L, Flicek, Paul, Nag, Rishi, Wong, Emily S, Blangero, John, Dyer, Thomas D, Bogomolov, Marina, Benjamini, Yoav, Weinstock, George M, Dewar, Ken, Sabatti, Chiara, Wilson, Richard K, Jentsch, J David, Warren, Wesley, Coppola, Giovanni, Woods, Roger P, and Freimer, Nelson B
Abstract: By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.
Published: 2017

27. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Author: Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Genome Standards Consortium, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017

28. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017
Full Text: View/download PDF

29. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Author: Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja
Abstract: We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
Published: 2017
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30. R2d2 drives selfish sweeps in the house mouse

Author: Didion, John P, Morgan, Andrew P, Yadgary, Liran, Bell, Timothy A, McMullan, Rachel C, de Solorzano, Lydia Ortiz, Britton-Davidian, Janice, Bult, Carol J, Campbell, Karl J, Castiglia, Riccardo, Ching, Yung-Hao, Chunco, Amanda J, Crowley, James J, Chesler, Elissa J, Förster, Daniel W, French, John E, Gabriel, Sofia I, Gatti, Daniel M, Garland, Theodore, Giagia-Athanasopoulou, Eva B, Giménez, Mabel D, Grize, Sofia A, Günduz, Islam, Holmes, Andrew, Hauffe, Heidi C, Herman, Jeremy S, Holt, James M, Hua, Kunjie, Jolley, Wesley J, Lindholm, Anna K, Lopez-Fuster, Maria J, Mitsainas, George, da Luz Mathias, Maria, McMillan, Leonard, da Graca Morgado Ramalhinho, Maria, Rehermann, Barbara, Rosshart, Stephan P, Searle, Jeremy B, Shiao, Meng-Shin, Solano, Emanuela, Svenson, Karen L, Thomas-Laemont, Patricia, Threadgill, David W, Ventura, Jacint, Weinstock, George M, Pomp, Daniel, Churchill, Gary A, de Villena, Fernando Pardo-Manuel, Didion, John P, Morgan, Andrew P, Yadgary, Liran, Bell, Timothy A, McMullan, Rachel C, de Solorzano, Lydia Ortiz, Britton-Davidian, Janice, Bult, Carol J, Campbell, Karl J, Castiglia, Riccardo, Ching, Yung-Hao, Chunco, Amanda J, Crowley, James J, Chesler, Elissa J, Förster, Daniel W, French, John E, Gabriel, Sofia I, Gatti, Daniel M, Garland, Theodore, Giagia-Athanasopoulou, Eva B, Giménez, Mabel D, Grize, Sofia A, Günduz, Islam, Holmes, Andrew, Hauffe, Heidi C, Herman, Jeremy S, Holt, James M, Hua, Kunjie, Jolley, Wesley J, Lindholm, Anna K, Lopez-Fuster, Maria J, Mitsainas, George, da Luz Mathias, Maria, McMillan, Leonard, da Graca Morgado Ramalhinho, Maria, Rehermann, Barbara, Rosshart, Stephan P, Searle, Jeremy B, Shiao, Meng-Shin, Solano, Emanuela, Svenson, Karen L, Thomas-Laemont, Patricia, Threadgill, David W, Ventura, Jacint, Weinstock, George M, Pomp, Daniel, Churchill, Gary A, and de Villena, Fernando Pardo-Manuel
Abstract: A selective sweep is the result of strong positive selection driving newly occurring or standing genetic variants to fixation, and can dramatically alter the pattern and distribution of allelic diversity in a population. Population-level sequencing data have enabled discoveries of selective sweeps associated with genes involved in recent adaptations in many species. In contrast, much debate but little evidence addresses whether “selfish” genes are capable of fixation – thereby leaving signatures identical to classical selective sweeps – despite being neutral or deleterious to organismal fitness. We previously described R2d2, a large copy-number variant that causes non-random segregation of mouse Chromosome 2 in females due to meiotic drive. Here we show population-genetic data consistent with a selfish sweep driven by alleles of R2d2 with high copy number (R2d2HC) in natural populations. We replicate this finding in multiple closed breeding populations from six outbred backgrounds segregating for R2d2 alleles. We find that R2d2HC rapidly increases in frequency, and in most cases becomes fixed in significantly fewer generations than can be explained by genetic drift. R2d2HC is also associated with significantly reduced litter sizes in heterozygous mothers, making it a true selfish allele. Our data provide direct evidence of populations actively undergoing selfish sweeps, and demonstrate that meiotic drive can rapidly alter the genomic landscape in favor of mutations with neutral or even negative effects on overall Darwinian fitness. Further study will reveal the incidence of selfish sweeps, and will elucidate the relative contributions of selfish genes, adaptation and genetic drift to evolution.
Published: 2016

31. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis.

Author: Shi, Baochen, Shi, Baochen, Chang, Michaela, Martin, John, Mitreva, Makedonka, Lux, Renate, Klokkevold, Perry, Sodergren, Erica, Weinstock, George M, Haake, Susan K, Li, Huiying, Shi, Baochen, Shi, Baochen, Chang, Michaela, Martin, John, Mitreva, Makedonka, Lux, Renate, Klokkevold, Perry, Sodergren, Erica, Weinstock, George M, Haake, Susan K, and Li, Huiying
Abstract: UNLABELLED:The human microbiome influences and reflects the health or disease state of the host. Periodontitis, a disease affecting about half of American adults, is associated with alterations in the subgingival microbiome of individual tooth sites. Although it can be treated, the disease can reoccur and may progress without symptoms. Without prognostic markers, follow-up examinations are required to assess reoccurrence and disease progression and to determine the need for additional treatments. To better identify and predict the disease progression, we aim to determine whether the subgingival microbiome can serve as a diagnosis and prognosis indicator. Using metagenomic shotgun sequencing, we characterized the dynamic changes in the subgingival microbiome in periodontitis patients before and after treatment at the same tooth sites. At the taxonomic composition level, the periodontitis-associated microorganisms were significantly shifted from highly correlated in the diseased state to poorly correlated after treatment, suggesting that coordinated interactions among the pathogenic microorganisms are essential to disease pathogenesis. At the functional level, we identified disease-associated pathways that were significantly altered in relative abundance in the two states. Furthermore, using the subgingival microbiome profile, we were able to classify the samples to their clinical states with an accuracy of 81.1%. Follow-up clinical examination of the sampled sites supported the predictive power of the microbiome profile on disease progression. Our study revealed the dynamic changes in the subgingival microbiome contributing to periodontitis and suggested potential clinical applications of monitoring the subgingival microbiome as an indicator in disease diagnosis and prognosis. IMPORTANCE:Periodontitis is a common oral disease. Although it can be treated, the disease may reoccur without obvious symptoms. Current clinical examination parameters are useful in disease di
Published: 2015

32. Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits.

Author: Huang, Yu S, Huang, Yu S, Ramensky, Vasily, Service, Susan K, Jasinska, Anna J, Jung, Yoon, Choi, Oi-Wa, Cantor, Rita M, Juretic, Nikoleta, Wasserscheid, Jessica, Kaplan, Jay R, Jorgensen, Matthew J, Dyer, Thomas D, Dewar, Ken, Blangero, John, Wilson, Richard K, Warren, Wesley, Weinstock, George M, Freimer, Nelson B, Huang, Yu S, Huang, Yu S, Ramensky, Vasily, Service, Susan K, Jasinska, Anna J, Jung, Yoon, Choi, Oi-Wa, Cantor, Rita M, Juretic, Nikoleta, Wasserscheid, Jessica, Kaplan, Jay R, Jorgensen, Matthew J, Dyer, Thomas D, Dewar, Ken, Blangero, John, Wilson, Richard K, Warren, Wesley, Weinstock, George M, and Freimer, Nelson B
Abstract: BackgroundWe report here the first genome-wide high-resolution polymorphism resource for non-human primate (NHP) association and linkage studies, constructed for the Caribbean-origin vervet monkey, or African green monkey (Chlorocebus aethiops sabaeus), one of the most widely used NHPs in biomedical research. We generated this resource by whole genome sequencing (WGS) of monkeys from the Vervet Research Colony (VRC), an NIH-supported research resource for which extensive phenotypic data are available.ResultsWe identified genome-wide single nucleotide polymorphisms (SNPs) by WGS of 721 members of an extended pedigree from the VRC. From high-depth WGS data we identified more than 4 million polymorphic unequivocal segregating sites; by pruning these SNPs based on heterozygosity, quality control filters, and the degree of linkage disequilibrium (LD) between SNPs, we constructed genome-wide panels suitable for genetic association (about 500,000 SNPs) and linkage analysis (about 150,000 SNPs). To further enhance the utility of these resources for linkage analysis, we used a further pruned subset of the linkage panel to generate multipoint identity by descent matrices.ConclusionsThe genetic and phenotypic resources now available for the VRC and other Caribbean-origin vervets enable their use for genetic investigation of traits relevant to human diseases.
Published: 2015

33. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis.

Author: Shi, Baochen, Blaser, Martin J1, Shi, Baochen, Chang, Michaela, Martin, John, Mitreva, Makedonka, Lux, Renate, Klokkevold, Perry, Sodergren, Erica, Weinstock, George M, Haake, Susan K, Li, Huiying, Shi, Baochen, Blaser, Martin J1, Shi, Baochen, Chang, Michaela, Martin, John, Mitreva, Makedonka, Lux, Renate, Klokkevold, Perry, Sodergren, Erica, Weinstock, George M, Haake, Susan K, and Li, Huiying
Abstract: UNLABELLED:The human microbiome influences and reflects the health or disease state of the host. Periodontitis, a disease affecting about half of American adults, is associated with alterations in the subgingival microbiome of individual tooth sites. Although it can be treated, the disease can reoccur and may progress without symptoms. Without prognostic markers, follow-up examinations are required to assess reoccurrence and disease progression and to determine the need for additional treatments. To better identify and predict the disease progression, we aim to determine whether the subgingival microbiome can serve as a diagnosis and prognosis indicator. Using metagenomic shotgun sequencing, we characterized the dynamic changes in the subgingival microbiome in periodontitis patients before and after treatment at the same tooth sites. At the taxonomic composition level, the periodontitis-associated microorganisms were significantly shifted from highly correlated in the diseased state to poorly correlated after treatment, suggesting that coordinated interactions among the pathogenic microorganisms are essential to disease pathogenesis. At the functional level, we identified disease-associated pathways that were significantly altered in relative abundance in the two states. Furthermore, using the subgingival microbiome profile, we were able to classify the samples to their clinical states with an accuracy of 81.1%. Follow-up clinical examination of the sampled sites supported the predictive power of the microbiome profile on disease progression. Our study revealed the dynamic changes in the subgingival microbiome contributing to periodontitis and suggested potential clinical applications of monitoring the subgingival microbiome as an indicator in disease diagnosis and prognosis. IMPORTANCE:Periodontitis is a common oral disease. Although it can be treated, the disease may reoccur without obvious symptoms. Current clinical examination parameters are useful in disease di
Published: 2015

34. Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits.

Author: Huang, Yu S, Huang, Yu S, Ramensky, Vasily, Service, Susan K, Jasinska, Anna J, Jung, Yoon, Choi, Oi-Wa, Cantor, Rita M, Juretic, Nikoleta, Wasserscheid, Jessica, Kaplan, Jay R, Jorgensen, Matthew J, Dyer, Thomas D, Dewar, Ken, Blangero, John, Wilson, Richard K, Warren, Wesley, Weinstock, George M, Freimer, Nelson B, Huang, Yu S, Huang, Yu S, Ramensky, Vasily, Service, Susan K, Jasinska, Anna J, Jung, Yoon, Choi, Oi-Wa, Cantor, Rita M, Juretic, Nikoleta, Wasserscheid, Jessica, Kaplan, Jay R, Jorgensen, Matthew J, Dyer, Thomas D, Dewar, Ken, Blangero, John, Wilson, Richard K, Warren, Wesley, Weinstock, George M, and Freimer, Nelson B
Abstract: BackgroundWe report here the first genome-wide high-resolution polymorphism resource for non-human primate (NHP) association and linkage studies, constructed for the Caribbean-origin vervet monkey, or African green monkey (Chlorocebus aethiops sabaeus), one of the most widely used NHPs in biomedical research. We generated this resource by whole genome sequencing (WGS) of monkeys from the Vervet Research Colony (VRC), an NIH-supported research resource for which extensive phenotypic data are available.ResultsWe identified genome-wide single nucleotide polymorphisms (SNPs) by WGS of 721 members of an extended pedigree from the VRC. From high-depth WGS data we identified more than 4 million polymorphic unequivocal segregating sites; by pruning these SNPs based on heterozygosity, quality control filters, and the degree of linkage disequilibrium (LD) between SNPs, we constructed genome-wide panels suitable for genetic association (about 500,000 SNPs) and linkage analysis (about 150,000 SNPs). To further enhance the utility of these resources for linkage analysis, we used a further pruned subset of the linkage panel to generate multipoint identity by descent matrices.ConclusionsThe genetic and phenotypic resources now available for the VRC and other Caribbean-origin vervets enable their use for genetic investigation of traits relevant to human diseases.
Published: 2015

35. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Author: Beck, James M, Beck, James M, Schloss, Patrick D, Venkataraman, Arvind, Twigg, Homer, Jablonski, Kathleen A, Bushman, Frederic D, Campbell, Thomas B, Charlson, Emily S, Collman, Ronald G, Crothers, Kristina, Curtis, Jeffrey L, Drews, Kimberly L, Flores, Sonia C, Fontenot, Andrew P, Foulkes, Mary A, Frank, Ian, Ghedin, Elodie, Huang, Laurence, Lynch, Susan V, Morris, Alison, Palmer, Brent E, Schmidt, Thomas M, Sodergren, Erica, Weinstock, George M, Young, Vincent B, Lung HIV Microbiome Project, Beck, James M, Beck, James M, Schloss, Patrick D, Venkataraman, Arvind, Twigg, Homer, Jablonski, Kathleen A, Bushman, Frederic D, Campbell, Thomas B, Charlson, Emily S, Collman, Ronald G, Crothers, Kristina, Curtis, Jeffrey L, Drews, Kimberly L, Flores, Sonia C, Fontenot, Andrew P, Foulkes, Mary A, Frank, Ian, Ghedin, Elodie, Huang, Laurence, Lynch, Susan V, Morris, Alison, Palmer, Brent E, Schmidt, Thomas M, Sodergren, Erica, Weinstock, George M, Young, Vincent B, and Lung HIV Microbiome Project
Abstract: RationaleImproved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear.ObjectivesWe determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects.MethodsParticipating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38).Measurements and main resultsMicrobial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects.ConclusionsThe overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
Published: 2015

36. The genome of the vervet (Chlorocebus aethiops sabaeus).

Author: Warren, Wesley C, Warren, Wesley C, Jasinska, Anna J, García-Pérez, Raquel, Svardal, Hannes, Tomlinson, Chad, Rocchi, Mariano, Archidiacono, Nicoletta, Capozzi, Oronzo, Minx, Patrick, Montague, Michael J, Kyung, Kim, Hillier, LaDeana W, Kremitzki, Milinn, Graves, Tina, Chiang, Colby, Hughes, Jennifer, Tran, Nam, Huang, Yu, Ramensky, Vasily, Choi, Oi-Wa, Jung, Yoon J, Schmitt, Christopher A, Juretic, Nikoleta, Wasserscheid, Jessica, Turner, Trudy R, Wiseman, Roger W, Tuscher, Jennifer J, Karl, Julie A, Schmitz, Jörn E, Zahn, Roland, O'Connor, David H, Redmond, Eugene, Nisbett, Alex, Jacquelin, Béatrice, Müller-Trutwin, Michaela C, Brenchley, Jason M, Dione, Michel, Antonio, Martin, Schroth, Gary P, Kaplan, Jay R, Jorgensen, Matthew J, Thomas, Gregg WC, Hahn, Matthew W, Raney, Brian J, Aken, Bronwen, Nag, Rishi, Schmitz, Juergen, Churakov, Gennady, Noll, Angela, Stanyon, Roscoe, Webb, David, Thibaud-Nissen, Francoise, Nordborg, Magnus, Marques-Bonet, Tomas, Dewar, Ken, Weinstock, George M, Wilson, Richard K, Freimer, Nelson B, Warren, Wesley C, Warren, Wesley C, Jasinska, Anna J, García-Pérez, Raquel, Svardal, Hannes, Tomlinson, Chad, Rocchi, Mariano, Archidiacono, Nicoletta, Capozzi, Oronzo, Minx, Patrick, Montague, Michael J, Kyung, Kim, Hillier, LaDeana W, Kremitzki, Milinn, Graves, Tina, Chiang, Colby, Hughes, Jennifer, Tran, Nam, Huang, Yu, Ramensky, Vasily, Choi, Oi-Wa, Jung, Yoon J, Schmitt, Christopher A, Juretic, Nikoleta, Wasserscheid, Jessica, Turner, Trudy R, Wiseman, Roger W, Tuscher, Jennifer J, Karl, Julie A, Schmitz, Jörn E, Zahn, Roland, O'Connor, David H, Redmond, Eugene, Nisbett, Alex, Jacquelin, Béatrice, Müller-Trutwin, Michaela C, Brenchley, Jason M, Dione, Michel, Antonio, Martin, Schroth, Gary P, Kaplan, Jay R, Jorgensen, Matthew J, Thomas, Gregg WC, Hahn, Matthew W, Raney, Brian J, Aken, Bronwen, Nag, Rishi, Schmitz, Juergen, Churakov, Gennady, Noll, Angela, Stanyon, Roscoe, Webb, David, Thibaud-Nissen, Francoise, Nordborg, Magnus, Marques-Bonet, Tomas, Dewar, Ken, Weinstock, George M, Wilson, Richard K, and Freimer, Nelson B
Abstract: We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations.
Published: 2015

37. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.

Author: Deng, Xiangyu, Deng, Xiangyu, Desai, Prerak T, den Bakker, Henk C, Mikoleit, Matthew, Tolar, Beth, Trees, Eija, Hendriksen, Rene S, Frye, Jonathan G, Porwollik, Steffen, Weimer, Bart C, Wiedmann, Martin, Weinstock, George M, Fields, Patricia I, McClelland, Michael, Deng, Xiangyu, Deng, Xiangyu, Desai, Prerak T, den Bakker, Henk C, Mikoleit, Matthew, Tolar, Beth, Trees, Eija, Hendriksen, Rene S, Frye, Jonathan G, Porwollik, Steffen, Weimer, Bart C, Wiedmann, Martin, Weinstock, George M, Fields, Patricia I, and McClelland, Michael
Abstract: Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s.
Published: 2014

38. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages.

Author: Deng, Xiangyu, Deng, Xiangyu, Desai, Prerak T, den Bakker, Henk C, Mikoleit, Matthew, Tolar, Beth, Trees, Eija, Hendriksen, Rene S, Frye, Jonathan G, Porwollik, Steffen, Weimer, Bart C, Wiedmann, Martin, Weinstock, George M, Fields, Patricia I, McClelland, Michael, Deng, Xiangyu, Deng, Xiangyu, Desai, Prerak T, den Bakker, Henk C, Mikoleit, Matthew, Tolar, Beth, Trees, Eija, Hendriksen, Rene S, Frye, Jonathan G, Porwollik, Steffen, Weimer, Bart C, Wiedmann, Martin, Weinstock, George M, Fields, Patricia I, and McClelland, Michael
Abstract: Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s.
Published: 2014

39. Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

Author: Deng, Xiangyu, Desai, Prerak T., den Bakker, Henk C., Mikoleit, Matthew, Tolar, Beth, Trees, Eija, Hendriksen, Rene S., Frye, Jonathan G., Porwollik, Steffen, Weimer, Bart C., Wiedmann, Martin, Weinstock, George M., Fields, Patricia I., McClelland, Michael, Deng, Xiangyu, Desai, Prerak T., den Bakker, Henk C., Mikoleit, Matthew, Tolar, Beth, Trees, Eija, Hendriksen, Rene S., Frye, Jonathan G., Porwollik, Steffen, Weimer, Bart C., Wiedmann, Martin, Weinstock, George M., Fields, Patricia I., and McClelland, Michael
Abstract: Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s.
Published: 2014

40. Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

Author: Morris, Alison, Morris, Alison, Beck, James M, Schloss, Patrick D, Campbell, Thomas B, Crothers, Kristina, Curtis, Jeffrey L, Flores, Sonia C, Fontenot, Andrew P, Ghedin, Elodie, Huang, Laurence, Jablonski, Kathleen, Kleerup, Eric, Lynch, Susan V, Sodergren, Erica, Twigg, Homer, Young, Vincent B, Bassis, Christine M, Venkataraman, Arvind, Schmidt, Thomas M, Weinstock, George M, Lung HIV Microbiome Project, Morris, Alison, Morris, Alison, Beck, James M, Schloss, Patrick D, Campbell, Thomas B, Crothers, Kristina, Curtis, Jeffrey L, Flores, Sonia C, Fontenot, Andrew P, Ghedin, Elodie, Huang, Laurence, Jablonski, Kathleen, Kleerup, Eric, Lynch, Susan V, Sodergren, Erica, Twigg, Homer, Young, Vincent B, Bassis, Christine M, Venkataraman, Arvind, Schmidt, Thomas M, Weinstock, George M, and Lung HIV Microbiome Project
Abstract: RationaleResults from 16S rDNA-encoding gene sequence-based, culture-independent techniques have led to conflicting conclusions about the composition of the lower respiratory tract microbiome.ObjectivesTo compare the microbiome of the upper and lower respiratory tract in healthy HIV-uninfected nonsmokers and smokers in a multicenter cohort.MethodsParticipants were nonsmokers and smokers without significant comorbidities. Oral washes and bronchoscopic alveolar lavages were collected in a standardized manner. Sequence analysis of bacterial 16S rRNA-encoding genes was performed, and the neutral model in community ecology was used to identify bacteria that were the most plausible members of a lung microbiome.Measurements and main resultsSixty-four participants were enrolled. Most bacteria identified in the lung were also in the mouth, but specific bacteria such as Enterobacteriaceae, Haemophilus, Methylobacterium, and Ralstonia species were disproportionally represented in the lungs compared with values predicted by the neutral model. Tropheryma was also in the lung, but not the mouth. Mouth communities differed between nonsmokers and smokers in species such as Porphyromonas, Neisseria, and Gemella, but lung bacterial populations did not.ConclusionsThis study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear in significantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.
Published: 2013

41. Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

Author: Lozupone, Catherine, Lozupone, Catherine, Cota-Gomez, Adela, Palmer, Brent E, Linderman, Derek J, Charlson, Emily S, Sodergren, Erica, Mitreva, Makedonka, Abubucker, Sahar, Martin, John, Yao, Guohui, Campbell, Thomas B, Flores, Sonia C, Ackerman, Gail, Stombaugh, Jesse, Ursell, Luke, Beck, James M, Curtis, Jeffrey L, Young, Vincent B, Lynch, Susan V, Huang, Laurence, Weinstock, George M, Knox, Kenneth S, Twigg, Homer, Morris, Alison, Ghedin, Elodie, Bushman, Frederic D, Collman, Ronald G, Knight, Rob, Fontenot, Andrew P, Lung HIV Microbiome Project, Lozupone, Catherine, Lozupone, Catherine, Cota-Gomez, Adela, Palmer, Brent E, Linderman, Derek J, Charlson, Emily S, Sodergren, Erica, Mitreva, Makedonka, Abubucker, Sahar, Martin, John, Yao, Guohui, Campbell, Thomas B, Flores, Sonia C, Ackerman, Gail, Stombaugh, Jesse, Ursell, Luke, Beck, James M, Curtis, Jeffrey L, Young, Vincent B, Lynch, Susan V, Huang, Laurence, Weinstock, George M, Knox, Kenneth S, Twigg, Homer, Morris, Alison, Ghedin, Elodie, Bushman, Frederic D, Collman, Ronald G, Knight, Rob, Fontenot, Andrew P, and Lung HIV Microbiome Project
Abstract: RationaleLung infections caused by opportunistic or virulent pathogens are a principal cause of morbidity and mortality in HIV infection. It is unknown whether HIV infection leads to changes in basal lung microflora, which may contribute to chronic pulmonary complications that increasingly are being recognized in individuals infected with HIV.ObjectivesTo determine whether the immunodeficiency associated with HIV infection resulted in alteration of the lung microbiota.MethodsWe used 16S ribosomal RNA targeted pyrosequencing and shotgun metagenomic sequencing to analyze bacterial gene sequences in bronchoalveolar lavage (BAL) and mouths of 82 HIV-positive and 77 HIV-negative subjects.Measurements and main resultsSequences representing Tropheryma whipplei, the etiologic agent of Whipple's disease, were significantly more frequent in BAL of HIV-positive compared with HIV-negative individuals. T. whipplei dominated the community (>50% of sequence reads) in 11 HIV-positive subjects, but only 1 HIV-negative individual (13.4 versus 1.3%; P = 0.0018). In 30 HIV-positive individuals sampled longitudinally, antiretroviral therapy resulted in a significantly reduced relative abundance of T. whipplei in the lung. Shotgun metagenomic sequencing was performed on eight BAL samples dominated by T. whipplei 16S ribosomal RNA. Whole genome assembly of pooled reads showed that uncultured lung-derived T. whipplei had similar gene content to two isolates obtained from subjects with Whipple's disease.ConclusionsAsymptomatic subjects with HIV infection have unexpected colonization of the lung by T. whipplei, which is reduced by effective antiretroviral therapy and merits further study for a potential pathogenic role in chronic pulmonary complications of HIV infection.
Published: 2013

42. Propionibacterium acnes strain populations in the human skin microbiome associated with acne.

Author: Fitz-Gibbon, Sorel, Fitz-Gibbon, Sorel, Tomida, Shuta, Chiu, Bor-Han, Nguyen, Lin, Du, Christine, Liu, Minghsun, Elashoff, David, Erfe, Marie C, Loncaric, Anya, Kim, Jenny, Modlin, Robert L, Miller, Jeff F, Sodergren, Erica, Craft, Noah, Weinstock, George M, Li, Huiying, Fitz-Gibbon, Sorel, Fitz-Gibbon, Sorel, Tomida, Shuta, Chiu, Bor-Han, Nguyen, Lin, Du, Christine, Liu, Minghsun, Elashoff, David, Erfe, Marie C, Loncaric, Anya, Kim, Jenny, Modlin, Robert L, Miller, Jeff F, Sodergren, Erica, Craft, Noah, Weinstock, George M, and Li, Huiying
Abstract: The human skin microbiome has important roles in skin health and disease. However, bacterial population structure and diversity at the strain level is poorly understood. We compared the skin microbiome at the strain level and genome level of Propionibacterium acnes, a dominant skin commensal, between 49 acne patients and 52 healthy individuals by sampling the pilosebaceous units on their noses. Metagenomic analysis demonstrated that although the relative abundances of P. acnes were similar, the strain population structures were significantly different in the two cohorts. Certain strains were highly associated with acne, and other strains were enriched in healthy skin. By sequencing 66 previously unreported P. acnes strains and comparing 71 P. acnes genomes, we identified potential genetic determinants of various P. acnes strains in association with acne or health. Our analysis suggests that acquired DNA sequences and bacterial immune elements may have roles in determining virulence properties of P. acnes strains, and some could be future targets for therapeutic interventions. This study demonstrates a previously unreported paradigm of commensal strain populations that could explain the pathogenesis of human diseases. It underscores the importance of strain-level analysis of the human microbiome to define the role of commensals in health and disease.
Published: 2013

43. Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

Author: Morris, Alison, Morris, Alison, Beck, James M, Schloss, Patrick D, Campbell, Thomas B, Crothers, Kristina, Curtis, Jeffrey L, Flores, Sonia C, Fontenot, Andrew P, Ghedin, Elodie, Huang, Laurence, Jablonski, Kathleen, Kleerup, Eric, Lynch, Susan V, Sodergren, Erica, Twigg, Homer, Young, Vincent B, Bassis, Christine M, Venkataraman, Arvind, Schmidt, Thomas M, Weinstock, George M, Lung HIV Microbiome Project, Morris, Alison, Morris, Alison, Beck, James M, Schloss, Patrick D, Campbell, Thomas B, Crothers, Kristina, Curtis, Jeffrey L, Flores, Sonia C, Fontenot, Andrew P, Ghedin, Elodie, Huang, Laurence, Jablonski, Kathleen, Kleerup, Eric, Lynch, Susan V, Sodergren, Erica, Twigg, Homer, Young, Vincent B, Bassis, Christine M, Venkataraman, Arvind, Schmidt, Thomas M, Weinstock, George M, and Lung HIV Microbiome Project
Abstract: RationaleResults from 16S rDNA-encoding gene sequence-based, culture-independent techniques have led to conflicting conclusions about the composition of the lower respiratory tract microbiome.ObjectivesTo compare the microbiome of the upper and lower respiratory tract in healthy HIV-uninfected nonsmokers and smokers in a multicenter cohort.MethodsParticipants were nonsmokers and smokers without significant comorbidities. Oral washes and bronchoscopic alveolar lavages were collected in a standardized manner. Sequence analysis of bacterial 16S rRNA-encoding genes was performed, and the neutral model in community ecology was used to identify bacteria that were the most plausible members of a lung microbiome.Measurements and main resultsSixty-four participants were enrolled. Most bacteria identified in the lung were also in the mouth, but specific bacteria such as Enterobacteriaceae, Haemophilus, Methylobacterium, and Ralstonia species were disproportionally represented in the lungs compared with values predicted by the neutral model. Tropheryma was also in the lung, but not the mouth. Mouth communities differed between nonsmokers and smokers in species such as Porphyromonas, Neisseria, and Gemella, but lung bacterial populations did not.ConclusionsThis study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear in significantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.
Published: 2013

44. Widespread colonization of the lung by Tropheryma whipplei in HIV infection.

Author: Lozupone, Catherine, Lozupone, Catherine, Cota-Gomez, Adela, Palmer, Brent E, Linderman, Derek J, Charlson, Emily S, Sodergren, Erica, Mitreva, Makedonka, Abubucker, Sahar, Martin, John, Yao, Guohui, Campbell, Thomas B, Flores, Sonia C, Ackerman, Gail, Stombaugh, Jesse, Ursell, Luke, Beck, James M, Curtis, Jeffrey L, Young, Vincent B, Lynch, Susan V, Huang, Laurence, Weinstock, George M, Knox, Kenneth S, Twigg, Homer, Morris, Alison, Ghedin, Elodie, Bushman, Frederic D, Collman, Ronald G, Knight, Rob, Fontenot, Andrew P, Lung HIV Microbiome Project, Lozupone, Catherine, Lozupone, Catherine, Cota-Gomez, Adela, Palmer, Brent E, Linderman, Derek J, Charlson, Emily S, Sodergren, Erica, Mitreva, Makedonka, Abubucker, Sahar, Martin, John, Yao, Guohui, Campbell, Thomas B, Flores, Sonia C, Ackerman, Gail, Stombaugh, Jesse, Ursell, Luke, Beck, James M, Curtis, Jeffrey L, Young, Vincent B, Lynch, Susan V, Huang, Laurence, Weinstock, George M, Knox, Kenneth S, Twigg, Homer, Morris, Alison, Ghedin, Elodie, Bushman, Frederic D, Collman, Ronald G, Knight, Rob, Fontenot, Andrew P, and Lung HIV Microbiome Project
Abstract: RationaleLung infections caused by opportunistic or virulent pathogens are a principal cause of morbidity and mortality in HIV infection. It is unknown whether HIV infection leads to changes in basal lung microflora, which may contribute to chronic pulmonary complications that increasingly are being recognized in individuals infected with HIV.ObjectivesTo determine whether the immunodeficiency associated with HIV infection resulted in alteration of the lung microbiota.MethodsWe used 16S ribosomal RNA targeted pyrosequencing and shotgun metagenomic sequencing to analyze bacterial gene sequences in bronchoalveolar lavage (BAL) and mouths of 82 HIV-positive and 77 HIV-negative subjects.Measurements and main resultsSequences representing Tropheryma whipplei, the etiologic agent of Whipple's disease, were significantly more frequent in BAL of HIV-positive compared with HIV-negative individuals. T. whipplei dominated the community (>50% of sequence reads) in 11 HIV-positive subjects, but only 1 HIV-negative individual (13.4 versus 1.3%; P = 0.0018). In 30 HIV-positive individuals sampled longitudinally, antiretroviral therapy resulted in a significantly reduced relative abundance of T. whipplei in the lung. Shotgun metagenomic sequencing was performed on eight BAL samples dominated by T. whipplei 16S ribosomal RNA. Whole genome assembly of pooled reads showed that uncultured lung-derived T. whipplei had similar gene content to two isolates obtained from subjects with Whipple's disease.ConclusionsAsymptomatic subjects with HIV infection have unexpected colonization of the lung by T. whipplei, which is reduced by effective antiretroviral therapy and merits further study for a potential pathogenic role in chronic pulmonary complications of HIV infection.
Published: 2013

45. Propionibacterium acnes strain populations in the human skin microbiome associated with acne.

Author: Fitz-Gibbon, Sorel, Fitz-Gibbon, Sorel, Tomida, Shuta, Chiu, Bor-Han, Nguyen, Lin, Du, Christine, Liu, Minghsun, Elashoff, David, Erfe, Marie C, Loncaric, Anya, Kim, Jenny, Modlin, Robert L, Miller, Jeff F, Sodergren, Erica, Craft, Noah, Weinstock, George M, Li, Huiying, Fitz-Gibbon, Sorel, Fitz-Gibbon, Sorel, Tomida, Shuta, Chiu, Bor-Han, Nguyen, Lin, Du, Christine, Liu, Minghsun, Elashoff, David, Erfe, Marie C, Loncaric, Anya, Kim, Jenny, Modlin, Robert L, Miller, Jeff F, Sodergren, Erica, Craft, Noah, Weinstock, George M, and Li, Huiying
Abstract: The human skin microbiome has important roles in skin health and disease. However, bacterial population structure and diversity at the strain level is poorly understood. We compared the skin microbiome at the strain level and genome level of Propionibacterium acnes, a dominant skin commensal, between 49 acne patients and 52 healthy individuals by sampling the pilosebaceous units on their noses. Metagenomic analysis demonstrated that although the relative abundances of P. acnes were similar, the strain population structures were significantly different in the two cohorts. Certain strains were highly associated with acne, and other strains were enriched in healthy skin. By sequencing 66 previously unreported P. acnes strains and comparing 71 P. acnes genomes, we identified potential genetic determinants of various P. acnes strains in association with acne or health. Our analysis suggests that acquired DNA sequences and bacterial immune elements may have roles in determining virulence properties of P. acnes strains, and some could be future targets for therapeutic interventions. This study demonstrates a previously unreported paradigm of commensal strain populations that could explain the pathogenesis of human diseases. It underscores the importance of strain-level analysis of the human microbiome to define the role of commensals in health and disease.
Published: 2013

46. Genomic variation landscape of the human gut microbiome

Author: Schloissnig, Siegfried, Arumugam, Manimozhiyan, Sunagawa, Shinichi, Mitreva, Makedonka, Tap, Julien, Zhu, Ana, Waller, Alison, Mende, Daniel R, Kultima, Jens Roat, Martin, John, Kota, Karthik, Sunyaev, Shamil R, Weinstock, George M, Bork, Peer, Schloissnig, Siegfried, Arumugam, Manimozhiyan, Sunagawa, Shinichi, Mitreva, Makedonka, Tap, Julien, Zhu, Ana, Waller, Alison, Mende, Daniel R, Kultima, Jens Roat, Martin, John, Kota, Karthik, Sunyaev, Shamil R, Weinstock, George M, and Bork, Peer
Abstract: Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.
Published: 2013

47. Genomic variation landscape of the human gut microbiome

Author: Schloissnig, Siegfried, Arumugam, Manimozhiyan, Sunagawa, Shinichi, Mitreva, Makedonka, Tap, Julien, Zhu, Ana, Waller, Alison, Mende, Daniel R, Kultima, Jens Roat, Martin, John, Kota, Karthik, Sunyaev, Shamil R, Weinstock, George M, Bork, Peer, Schloissnig, Siegfried, Arumugam, Manimozhiyan, Sunagawa, Shinichi, Mitreva, Makedonka, Tap, Julien, Zhu, Ana, Waller, Alison, Mende, Daniel R, Kultima, Jens Roat, Martin, John, Kota, Karthik, Sunyaev, Shamil R, Weinstock, George M, and Bork, Peer
Abstract: Whereas large-scale efforts have rapidly advanced the understanding and practical impact of human genomic variation, the practical impact of variation is largely unexplored in the human microbiome. We therefore developed a framework for metagenomic variation analysis and applied it to 252 faecal metagenomes of 207 individuals from Europe and North America. Using 7.4 billion reads aligned to 101 reference species, we detected 10.3 million single nucleotide polymorphisms (SNPs), 107,991 short insertions/deletions, and 1,051 structural variants. The average ratio of non-synonymous to synonymous polymorphism rates of 0.11 was more variable between gut microbial species than across human hosts. Subjects sampled at varying time intervals exhibited individuality and temporal stability of SNP variation patterns, despite considerable composition changes of their gut microbiota. This indicates that individual-specific strains are not easily replaced and that an individual might have a unique metagenomic genotype, which may be exploitable for personalized diet or drug intake.
Published: 2013

48. A high-resolution map of human evolutionary constraint using 29 mammals

Author: Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoeldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J., Jaffe, David B., Jungreis, Irwin, Kent, W. James, Kostka, Dennis, Lara, Marcia, Martins, Andre L., Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., Kellis, Manolis, Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alfoeldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J., Jaffe, David B., Jungreis, Irwin, Kent, W. James, Kostka, Dennis, Lara, Marcia, Martins, Andre L., Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., and Kellis, Manolis
Abstract: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering similar to 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for similar to 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate-and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
Published: 2011
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49. A high-resolution map of human evolutionary constraint using 29 mammals.

Author: Lindblad-Toh, Kerstin, Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F, Parker, Brian J, Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D, Lowe, Craig B, Holloway, Alisha K, Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B, Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J, Rasmussen, Matthew D, Robinson, Jim, Stark, Alexander, Vilella, Albert J, Wen, Jiayu, Xie, Xiaohui, Zody, Michael C, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Chin, Chee Whye, Heiman, Dave, Nicol, Robert, Nusbaum, Chad, Young, Sarah, Wilkinson, Jane, Worley, Kim C, Kovar, Christie L, Muzny, Donna M, Gibbs, Richard A, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree, Andrew, Dihn, Huyen H, Fowler, Gerald, Jhangiani, Shalili, Joshi, Vandita, Lee, Sandra, Lewis, Lora R, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Warren, Wesley C, Mardis, Elaine R, Weinstock, George M, Wilson, Richard K, Genome Institute at Washington University, Delehaunty, Kim, Dooling, David, Fronik, Catrina, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Minx, Patrick, Sodergren, Erica, Birney, Ewan, Margulies, Elliott H, Herrero, Javier, Green, Eric D, Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S, Pedersen, Jakob S, Lander, Eric S, Kellis, Manolis, Lindblad-Toh, Kerstin, Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F, Parker, Brian J, Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D, Lowe, Craig B, Holloway, Alisha K, Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B, Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J, Rasmussen, Matthew D, Robinson, Jim, Stark, Alexander, Vilella, Albert J, Wen, Jiayu, Xie, Xiaohui, Zody, Michael C, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Chin, Chee Whye, Heiman, Dave, Nicol, Robert, Nusbaum, Chad, Young, Sarah, Wilkinson, Jane, Worley, Kim C, Kovar, Christie L, Muzny, Donna M, Gibbs, Richard A, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree, Andrew, Dihn, Huyen H, Fowler, Gerald, Jhangiani, Shalili, Joshi, Vandita, Lee, Sandra, Lewis, Lora R, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Warren, Wesley C, Mardis, Elaine R, Weinstock, George M, Wilson, Richard K, Genome Institute at Washington University, Delehaunty, Kim, Dooling, David, Fronik, Catrina, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Minx, Patrick, Sodergren, Erica, Birney, Ewan, Margulies, Elliott H, Herrero, Javier, Green, Eric D, Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S, Pedersen, Jakob S, Lander, Eric S, and Kellis, Manolis
Abstract: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
Published: 2011

50. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Author: Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R, Amaral-Zettler, Linda, Gilbert, Jack A, Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W, Blaser, Martin J, Bonazzi, Vivien, Booth, Tim, Bork, Peer, Bushman, Frederic D, Buttigieg, Pier Luigi, Chain, Patrick S G, Charlson, Emily, Costello, Elizabeth K, Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed A, Gallery, Rachel E, Gevers, Dirk, Gibbs, Richard A, Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I, Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kau, Andrew L, Kelley, Scott T, Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L, Legg, Teresa, Ley, Ruth E, Lozupone, Catherine A, Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara A, Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E, Nemergut, Diana, Neufeld, Josh D, Newbold, Lindsay K, Oliver, Anna E, Pace, Norman R, Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A, Assunta-Sansone, Susanna, Schloss, Patrick D, Schriml, Lynn, Sinha, Rohini, Smith, Michelle I, Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M, Ward, Doyle V, Weinstock, George M, Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R, Yatsunenko, Tanya, Glöckner, Frank Oliver, Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R, Amaral-Zettler, Linda, Gilbert, Jack A, Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W, Blaser, Martin J, Bonazzi, Vivien, Booth, Tim, Bork, Peer, Bushman, Frederic D, Buttigieg, Pier Luigi, Chain, Patrick S G, Charlson, Emily, Costello, Elizabeth K, Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed A, Gallery, Rachel E, Gevers, Dirk, Gibbs, Richard A, Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I, Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kau, Andrew L, Kelley, Scott T, Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L, Legg, Teresa, Ley, Ruth E, Lozupone, Catherine A, Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara A, Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E, Nemergut, Diana, Neufeld, Josh D, Newbold, Lindsay K, Oliver, Anna E, Pace, Norman R, Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A, Assunta-Sansone, Susanna, Schloss, Patrick D, Schriml, Lynn, Sinha, Rohini, Smith, Michelle I, Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M, Ward, Doyle V, Weinstock, George M, Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R, Yatsunenko, Tanya, and Glöckner, Frank Oliver
Abstract: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Published: 2011

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