Unraveling the functional dark matter through global metagenomics

Georgios A. Pavlopoulos; Fotis A. Baltoumas; Sirui Liu; Oguz Selvitopi; Antonio Pedro Camargo; Stephen Nayfach; Ariful Azad; Simon Roux; Lee Call; Natalia N. Ivanova; I. Min Chen; David Paez-Espino; Evangelos Karatzas; Silvia G. Acinas; Nathan Ahlgren; Graeme Attwood; Petr Baldrian; Timothy Berry; Jennifer M. Bhatnagar; Devaki Bhaya; Kay D. Bidle; Jeffrey L. Blanchard; Eric S. Boyd; Jennifer L. Bowen; Jeff Bowman; Susan H. Brawley; Eoin L. Brodie; Andreas Brune; Donald A. Bryant; Alison Buchan; Hinsby Cadillo-Quiroz; Barbara J. Campbell; Ricardo Cavicchioli; Peter F. Chuckran; Maureen Coleman; Sean Crowe; Daniel R. Colman; Cameron R. Currie; Jeff Dangl; Nathalie Delherbe; Vincent J. Denef; Paul Dijkstra; Daniel D. Distel; Emiley Eloe-Fadrosh; Kirsten Fisher; Christopher Francis; Aaron Garoutte; Amelie Gaudin; Lena Gerwick; Filipa Godoy-Vitorino; Peter Guerra; Jiarong Guo; Mussie Y. Habteselassie; Steven J. Hallam; Roland Hatzenpichler; Ute Hentschel; Matthias Hess; Ann M. Hirsch; Laura A. Hug; Jenni Hultman; Dana E. Hunt; Marcel Huntemann; William P. Inskeep; Timothy Y. James; Janet Jansson; Eric R. Johnston; Marina Kalyuzhnaya; Charlene N. Kelly; Robert M. Kelly; Jonathan L. Klassen; Klaus Nüsslein; Joel E. Kostka; Steven Lindow; Erik Lilleskov; Mackenzie Lynes; Rachel Mackelprang; Francis M. Martin; Olivia U. Mason; R. Michael McKay; Katherine McMahon; David A. Mead; Monica Medina; Laura K. Meredith; Thomas Mock; William W. Mohn; Mary Ann Moran; Alison Murray; Josh D. Neufeld; Rebecca Neumann; Jeanette M. Norton; Laila P. Partida-Martinez; Nicole Pietrasiak; Dale Pelletier; T. B.K. Reddy; Brandi Kiel Reese; Nicholas J. Reichart; Rebecca Reiss; Mak A. Saito; Daniel P. Schachtman; Rekha Seshadri; Ashley Shade; David Sherman; Rachel Simister; Holly Simon; James Stegen; Ramunas Stepanauskas; Matthew Sullivan; Dawn Y. Sumner; Hanno Teeling; Kimberlee Thamatrakoln; Kathleen Treseder; Susannah Tringe; Parag Vaishampayan; David L. Valentine; Nicholas B. Waldo; Mark P. Waldrop; David A. Walsh; David M. Ward; Michael Wilkins; Thea Whitman; Jamie Woolet; Tanja Woyke; Ioannis Iliopoulos; Konstantinos Konstantinidis; James M. Tiedje; Jennifer Pett-Ridge; David Baker; Axel Visel; Christos A. Ouzounis; Sergey Ovchinnikov; Aydin Buluç; Nikos C. Kyrpides

doi:10.1038/s41586-023-06583-7

Unraveling the functional dark matter through global metagenomics

Georgios A. Pavlopoulos, Fotis A. Baltoumas, Sirui Liu, Oguz Selvitopi, Antonio Pedro Camargo, Stephen Nayfach, Ariful Azad, Simon Roux, Lee Call, Natalia N. Ivanova, I. Min Chen, David Paez-Espino, Evangelos Karatzas, Silvia G. Acinas, Nathan Ahlgren, Graeme Attwood, Petr Baldrian, Timothy Berry, Jennifer M. Bhatnagar, Devaki BhayaKay D. Bidle, Jeffrey L. Blanchard, Eric S. Boyd, Jennifer L. Bowen, Jeff Bowman, Susan H. Brawley, Eoin L. Brodie, Andreas Brune, Donald A. Bryant, Alison Buchan, Hinsby Cadillo-Quiroz, Barbara J. Campbell, Ricardo Cavicchioli, Peter F. Chuckran, Maureen Coleman, Sean Crowe, Daniel R. Colman, Cameron R. Currie, Jeff Dangl, Nathalie Delherbe, Vincent J. Denef, Paul Dijkstra, Daniel D. Distel, Emiley Eloe-Fadrosh, Kirsten Fisher, Christopher Francis, Aaron Garoutte, Amelie Gaudin, Lena Gerwick, Filipa Godoy-Vitorino, Peter Guerra, Jiarong Guo, Mussie Y. Habteselassie, Steven J. Hallam, Roland Hatzenpichler, Ute Hentschel, Matthias Hess, Ann M. Hirsch, Laura A. Hug, Jenni Hultman, Dana E. Hunt, Marcel Huntemann, William P. Inskeep, Timothy Y. James, Janet Jansson, Eric R. Johnston, Marina Kalyuzhnaya, Charlene N. Kelly, Robert M. Kelly, Jonathan L. Klassen, Klaus Nüsslein, Joel E. Kostka, Steven Lindow, Erik Lilleskov, Mackenzie Lynes, Rachel Mackelprang, Francis M. Martin, Olivia U. Mason, R. Michael McKay, Katherine McMahon, David A. Mead, Monica Medina, Laura K. Meredith, Thomas Mock, William W. Mohn, Mary Ann Moran, Alison Murray, Josh D. Neufeld, Rebecca Neumann, Jeanette M. Norton, Laila P. Partida-Martinez, Nicole Pietrasiak, Dale Pelletier, T. B.K. Reddy, Brandi Kiel Reese, Nicholas J. Reichart, Rebecca Reiss, Mak A. Saito, Daniel P. Schachtman, Rekha Seshadri, Ashley Shade, David Sherman, Rachel Simister, Holly Simon, James Stegen, Ramunas Stepanauskas, Matthew Sullivan, Dawn Y. Sumner, Hanno Teeling, Kimberlee Thamatrakoln, Kathleen Treseder, Susannah Tringe, Parag Vaishampayan, David L. Valentine, Nicholas B. Waldo, Mark P. Waldrop, David A. Walsh, David M. Ward, Michael Wilkins, Thea Whitman, Jamie Woolet, Tanja Woyke, Ioannis Iliopoulos, Konstantinos Konstantinidis, James M. Tiedje, Jennifer Pett-Ridge, David Baker, Axel Visel, Christos A. Ouzounis, Sergey Ovchinnikov, Aydin Buluç, Nikos C. Kyrpides

Research output: Contribution to journal › Article › peer-review

31 Scopus citations

Abstract

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities^1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database³. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

Original language	English (US)
Pages (from-to)	594-602
Number of pages	9
Journal	Nature
Volume	622
Issue number	7983
DOIs	https://doi.org/10.1038/s41586-023-06583-7
State	Published - Oct 19 2023

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10.1038/s41586-023-06583-7

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Pavlopoulos, G. A., Baltoumas, F. A., Liu, S., Selvitopi, O., Camargo, A. P., Nayfach, S., Azad, A., Roux, S., Call, L., Ivanova, N. N., Chen, I. M., Paez-Espino, D., Karatzas, E., Acinas, S. G., Ahlgren, N., Attwood, G., Baldrian, P., Berry, T., Bhatnagar, J. M., ... Kyrpides, N. C. (2023). Unraveling the functional dark matter through global metagenomics. Nature, 622(7983), 594-602. https://doi.org/10.1038/s41586-023-06583-7

@article{b61a2f4d9c5044ad900b9ab63d8b719f,

title = "Unraveling the functional dark matter through global metagenomics",

abstract = "Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.",

author = "Pavlopoulos, {Georgios A.} and Baltoumas, {Fotis A.} and Sirui Liu and Oguz Selvitopi and Camargo, {Antonio Pedro} and Stephen Nayfach and Ariful Azad and Simon Roux and Lee Call and Ivanova, {Natalia N.} and Chen, {I. Min} and David Paez-Espino and Evangelos Karatzas and Acinas, {Silvia G.} and Nathan Ahlgren and Graeme Attwood and Petr Baldrian and Timothy Berry and Bhatnagar, {Jennifer M.} and Devaki Bhaya and Bidle, {Kay D.} and Blanchard, {Jeffrey L.} and Boyd, {Eric S.} and Bowen, {Jennifer L.} and Jeff Bowman and Brawley, {Susan H.} and Brodie, {Eoin L.} and Andreas Brune and Bryant, {Donald A.} and Alison Buchan and Hinsby Cadillo-Quiroz and Campbell, {Barbara J.} and Ricardo Cavicchioli and Chuckran, {Peter F.} and Maureen Coleman and Sean Crowe and Colman, {Daniel R.} and Currie, {Cameron R.} and Jeff Dangl and Nathalie Delherbe and Denef, {Vincent J.} and Paul Dijkstra and Distel, {Daniel D.} and Emiley Eloe-Fadrosh and Kirsten Fisher and Christopher Francis and Aaron Garoutte and Amelie Gaudin and Lena Gerwick and Filipa Godoy-Vitorino and Peter Guerra and Jiarong Guo and Habteselassie, {Mussie Y.} and Hallam, {Steven J.} and Roland Hatzenpichler and Ute Hentschel and Matthias Hess and Hirsch, {Ann M.} and Hug, {Laura A.} and Jenni Hultman and Hunt, {Dana E.} and Marcel Huntemann and Inskeep, {William P.} and James, {Timothy Y.} and Janet Jansson and Johnston, {Eric R.} and Marina Kalyuzhnaya and Kelly, {Charlene N.} and Kelly, {Robert M.} and Klassen, {Jonathan L.} and Klaus N{\"u}sslein and Kostka, {Joel E.} and Steven Lindow and Erik Lilleskov and Mackenzie Lynes and Rachel Mackelprang and Martin, {Francis M.} and Mason, {Olivia U.} and McKay, {R. Michael} and Katherine McMahon and Mead, {David A.} and Monica Medina and Meredith, {Laura K.} and Thomas Mock and Mohn, {William W.} and Moran, {Mary Ann} and Alison Murray and Neufeld, {Josh D.} and Rebecca Neumann and Norton, {Jeanette M.} and Partida-Martinez, {Laila P.} and Nicole Pietrasiak and Dale Pelletier and Reddy, {T. B.K.} and Reese, {Brandi Kiel} and Reichart, {Nicholas J.} and Rebecca Reiss and Saito, {Mak A.} and Schachtman, {Daniel P.} and Rekha Seshadri and Ashley Shade and David Sherman and Rachel Simister and Holly Simon and James Stegen and Ramunas Stepanauskas and Matthew Sullivan and Sumner, {Dawn Y.} and Hanno Teeling and Kimberlee Thamatrakoln and Kathleen Treseder and Susannah Tringe and Parag Vaishampayan and Valentine, {David L.} and Waldo, {Nicholas B.} and Waldrop, {Mark P.} and Walsh, {David A.} and Ward, {David M.} and Michael Wilkins and Thea Whitman and Jamie Woolet and Tanja Woyke and Ioannis Iliopoulos and Konstantinos Konstantinidis and Tiedje, {James M.} and Jennifer Pett-Ridge and David Baker and Axel Visel and Ouzounis, {Christos A.} and Sergey Ovchinnikov and Aydin Bulu{\c c} and Kyrpides, {Nikos C.}",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s).",

year = "2023",

month = oct,

day = "19",

doi = "10.1038/s41586-023-06583-7",

language = "English (US)",

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pages = "594--602",

journal = "Nature",

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Pavlopoulos, GA, Baltoumas, FA, Liu, S, Selvitopi, O, Camargo, AP, Nayfach, S, Azad, A, Roux, S, Call, L, Ivanova, NN, Chen, IM, Paez-Espino, D, Karatzas, E, Acinas, SG, Ahlgren, N, Attwood, G, Baldrian, P, Berry, T, Bhatnagar, JM, Bhaya, D, Bidle, KD, Blanchard, JL, Boyd, ES, Bowen, JL, Bowman, J, Brawley, SH, Brodie, EL, Brune, A, Bryant, DA, Buchan, A, Cadillo-Quiroz, H, Campbell, BJ, Cavicchioli, R, Chuckran, PF, Coleman, M, Crowe, S, Colman, DR, Currie, CR, Dangl, J, Delherbe, N, Denef, VJ, Dijkstra, P, Distel, DD, Eloe-Fadrosh, E, Fisher, K, Francis, C, Garoutte, A, Gaudin, A, Gerwick, L, Godoy-Vitorino, F, Guerra, P, Guo, J, Habteselassie, MY, Hallam, SJ, Hatzenpichler, R, Hentschel, U, Hess, M, Hirsch, AM, Hug, LA, Hultman, J, Hunt, DE, Huntemann, M, Inskeep, WP, James, TY, Jansson, J, Johnston, ER, Kalyuzhnaya, M, Kelly, CN, Kelly, RM, Klassen, JL, Nüsslein, K, Kostka, JE, Lindow, S, Lilleskov, E, Lynes, M, Mackelprang, R, Martin, FM, Mason, OU, McKay, RM, McMahon, K, Mead, DA, Medina, M, Meredith, LK, Mock, T, Mohn, WW, Moran, MA, Murray, A, Neufeld, JD, Neumann, R, Norton, JM, Partida-Martinez, LP, Pietrasiak, N, Pelletier, D, Reddy, TBK, Reese, BK, Reichart, NJ, Reiss, R, Saito, MA, Schachtman, DP, Seshadri, R, Shade, A, Sherman, D, Simister, R, Simon, H, Stegen, J, Stepanauskas, R, Sullivan, M, Sumner, DY, Teeling, H, Thamatrakoln, K, Treseder, K, Tringe, S, Vaishampayan, P, Valentine, DL, Waldo, NB, Waldrop, MP, Walsh, DA, Ward, DM, Wilkins, M, Whitman, T, Woolet, J, Woyke, T, Iliopoulos, I, Konstantinidis, K, Tiedje, JM, Pett-Ridge, J, Baker, D, Visel, A, Ouzounis, CA, Ovchinnikov, S, Buluç, A & Kyrpides, NC 2023, 'Unraveling the functional dark matter through global metagenomics', Nature, vol. 622, no. 7983, pp. 594-602. https://doi.org/10.1038/s41586-023-06583-7

TY - JOUR

T1 - Unraveling the functional dark matter through global metagenomics

AU - Pavlopoulos, Georgios A.

AU - Baltoumas, Fotis A.

AU - Liu, Sirui

AU - Selvitopi, Oguz

AU - Camargo, Antonio Pedro

AU - Nayfach, Stephen

AU - Azad, Ariful

AU - Roux, Simon

AU - Call, Lee

AU - Ivanova, Natalia N.

AU - Chen, I. Min

AU - Paez-Espino, David

AU - Karatzas, Evangelos

AU - Acinas, Silvia G.

AU - Ahlgren, Nathan

AU - Attwood, Graeme

AU - Baldrian, Petr

AU - Berry, Timothy

AU - Bhatnagar, Jennifer M.

AU - Bhaya, Devaki

AU - Bidle, Kay D.

AU - Blanchard, Jeffrey L.

AU - Boyd, Eric S.

AU - Bowen, Jennifer L.

AU - Bowman, Jeff

AU - Brawley, Susan H.

AU - Brodie, Eoin L.

AU - Brune, Andreas

AU - Bryant, Donald A.

AU - Buchan, Alison

AU - Cadillo-Quiroz, Hinsby

AU - Campbell, Barbara J.

AU - Cavicchioli, Ricardo

AU - Chuckran, Peter F.

AU - Coleman, Maureen

AU - Crowe, Sean

AU - Colman, Daniel R.

AU - Currie, Cameron R.

AU - Dangl, Jeff

AU - Delherbe, Nathalie

AU - Denef, Vincent J.

AU - Dijkstra, Paul

AU - Distel, Daniel D.

AU - Eloe-Fadrosh, Emiley

AU - Fisher, Kirsten

AU - Francis, Christopher

AU - Garoutte, Aaron

AU - Gaudin, Amelie

AU - Gerwick, Lena

AU - Godoy-Vitorino, Filipa

AU - Guerra, Peter

AU - Guo, Jiarong

AU - Habteselassie, Mussie Y.

AU - Hallam, Steven J.

AU - Hatzenpichler, Roland

AU - Hentschel, Ute

AU - Hess, Matthias

AU - Hirsch, Ann M.

AU - Hug, Laura A.

AU - Hultman, Jenni

AU - Hunt, Dana E.

AU - Huntemann, Marcel

AU - Inskeep, William P.

AU - James, Timothy Y.

AU - Jansson, Janet

AU - Johnston, Eric R.

AU - Kalyuzhnaya, Marina

AU - Kelly, Charlene N.

AU - Kelly, Robert M.

AU - Klassen, Jonathan L.

AU - Nüsslein, Klaus

AU - Kostka, Joel E.

AU - Lindow, Steven

AU - Lilleskov, Erik

AU - Lynes, Mackenzie

AU - Mackelprang, Rachel

AU - Martin, Francis M.

AU - Mason, Olivia U.

AU - McKay, R. Michael

AU - McMahon, Katherine

AU - Mead, David A.

AU - Medina, Monica

AU - Meredith, Laura K.

AU - Mock, Thomas

AU - Mohn, William W.

AU - Moran, Mary Ann

AU - Murray, Alison

AU - Neufeld, Josh D.

AU - Neumann, Rebecca

AU - Norton, Jeanette M.

AU - Partida-Martinez, Laila P.

AU - Pietrasiak, Nicole

AU - Pelletier, Dale

AU - Reddy, T. B.K.

AU - Reese, Brandi Kiel

AU - Reichart, Nicholas J.

AU - Reiss, Rebecca

AU - Saito, Mak A.

AU - Schachtman, Daniel P.

AU - Seshadri, Rekha

AU - Shade, Ashley

AU - Sherman, David

AU - Simister, Rachel

AU - Simon, Holly

AU - Stegen, James

AU - Stepanauskas, Ramunas

AU - Sullivan, Matthew

AU - Sumner, Dawn Y.

AU - Teeling, Hanno

AU - Thamatrakoln, Kimberlee

AU - Treseder, Kathleen

AU - Tringe, Susannah

AU - Vaishampayan, Parag

AU - Valentine, David L.

AU - Waldo, Nicholas B.

AU - Waldrop, Mark P.

AU - Walsh, David A.

AU - Ward, David M.

AU - Wilkins, Michael

AU - Whitman, Thea

AU - Woolet, Jamie

AU - Woyke, Tanja

AU - Iliopoulos, Ioannis

AU - Konstantinidis, Konstantinos

AU - Tiedje, James M.

AU - Pett-Ridge, Jennifer

AU - Baker, David

AU - Visel, Axel

AU - Ouzounis, Christos A.

AU - Ovchinnikov, Sergey

AU - Buluç, Aydin

AU - Kyrpides, Nikos C.

PY - 2023/10/19

Y1 - 2023/10/19

N2 - Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

AB - Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.

UR - http://www.scopus.com/inward/record.url?scp=85173864812&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85173864812&partnerID=8YFLogxK

U2 - 10.1038/s41586-023-06583-7

DO - 10.1038/s41586-023-06583-7

M3 - Article

C2 - 37821698

AN - SCOPUS:85173864812

SN - 0028-0836

VL - 622

SP - 594

EP - 602

JO - Nature

JF - Nature

IS - 7983

ER -

Unraveling the functional dark matter through global metagenomics

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