Challenges in microbial ecology: building predictive understanding of community function and dynamics

Stefanie Widder; Rosalind J Allen; Thomas Pfeiffer; Thomas P Curtis; Carsten Wiuf; William T Sloan; Otto X Cordero; Sam P Brown; Babak Momeni; Wenying Shou; Helen Kettle; Harry J Flint; Andreas F Haas; Béatrice Laroche; Jan-Ulrich Kreft; Paul B Rainey; Shiri Freilich; Stefan Schuster; Kim Milferstedt; Jan R van der Meer; Tobias Groszkopf; Jef Huisman; Andrew Free; Cristian Picioreanu; Christopher Quince; Isaac Klapper; Simon Labarthe; Barth F Smets; Harris Wang; Orkun S Soyer; Isaac Newton Institute Fellows

doi:10.1038/ismej.2016.45

Challenges in microbial ecology: building predictive understanding of community function and dynamics

Stefanie Widder, Rosalind J Allen, Thomas Pfeiffer, Thomas P Curtis, Carsten Wiuf, William T Sloan, Otto X Cordero, Sam P Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry J Flint, Andreas F Haas, Béatrice Laroche, Jan-Ulrich Kreft, Paul B Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan R van der MeerTobias Groszkopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth F Smets, Harris Wang, Orkun S Soyer, Isaac Newton Institute Fellows

The Rowett Institute of Nutrition and Health

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Abstract

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.The ISME Journal advance online publication, 29 March 2016; doi:10.1038/ismej.2016.45.

Original language	English
Pages (from-to)	2557-2568
Number of pages	12
Journal	The ISME Journal
Volume	10
Issue number	11
Early online date	29 Mar 2016
DOIs	https://doi.org/10.1038/ismej.2016.45
Publication status	Published - Nov 2016

Bibliographical note

Acknowledgements
We thank the Isaac Newton Institute of Mathematical Sciences for hosting the programme ‘Understanding microbial communities: structure, function dynamics’, which made this paper possible. This programme was partially funded by the Biotechnology and Biological Sciences Research Council and the US Army Research Office under grant number W911NF-14-1-0445. We thank all participants of the programme for inspiring discussions, and Aglika Gungova and Stela Ilieva for assistance with the figures.

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Challenges in microbial ecology: building predictive understanding of community function and dynamics
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Widder, S., Allen, R. J., Pfeiffer, T., Curtis, T. P., Wiuf, C., Sloan, W. T., Cordero, O. X., Brown, S. P., Momeni, B., Shou, W., Kettle, H., Flint, H. J., Haas, A. F., Laroche, B., Kreft, J.-U., Rainey, P. B., Freilich, S., Schuster, S., Milferstedt, K., ... Isaac Newton Institute Fellows (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME Journal, 10(11), 2557-2568. https://doi.org/10.1038/ismej.2016.45

Widder, S, Allen, RJ, Pfeiffer, T, Curtis, TP, Wiuf, C, Sloan, WT, Cordero, OX, Brown, SP, Momeni, B, Shou, W, Kettle, H, Flint, HJ, Haas, AF, Laroche, B, Kreft, J-U, Rainey, PB, Freilich, S, Schuster, S, Milferstedt, K, van der Meer, JR, Groszkopf, T, Huisman, J, Free, A, Picioreanu, C, Quince, C, Klapper, I, Labarthe, S, Smets, BF, Wang, H, Soyer, OS & Isaac Newton Institute Fellows 2016, 'Challenges in microbial ecology: building predictive understanding of community function and dynamics', The ISME Journal, vol. 10, no. 11, pp. 2557-2568. https://doi.org/10.1038/ismej.2016.45

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title = "Challenges in microbial ecology: building predictive understanding of community function and dynamics",

abstract = "The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.The ISME Journal advance online publication, 29 March 2016; doi:10.1038/ismej.2016.45.",

author = "Stefanie Widder and Allen, {Rosalind J} and Thomas Pfeiffer and Curtis, {Thomas P} and Carsten Wiuf and Sloan, {William T} and Cordero, {Otto X} and Brown, {Sam P} and Babak Momeni and Wenying Shou and Helen Kettle and Flint, {Harry J} and Haas, {Andreas F} and B{\'e}atrice Laroche and Jan-Ulrich Kreft and Rainey, {Paul B} and Shiri Freilich and Stefan Schuster and Kim Milferstedt and {van der Meer}, {Jan R} and Tobias Groszkopf and Jef Huisman and Andrew Free and Cristian Picioreanu and Christopher Quince and Isaac Klapper and Simon Labarthe and Smets, {Barth F} and Harris Wang and Soyer, {Orkun S} and {Isaac Newton Institute Fellows}",

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AU - Sloan, William T

AU - Cordero, Otto X

AU - Brown, Sam P

AU - Momeni, Babak

AU - Shou, Wenying

AU - Kettle, Helen

AU - Flint, Harry J

AU - Haas, Andreas F

AU - Laroche, Béatrice

AU - Kreft, Jan-Ulrich

AU - Rainey, Paul B

AU - Freilich, Shiri

AU - Schuster, Stefan

AU - Milferstedt, Kim

AU - van der Meer, Jan R

AU - Groszkopf, Tobias

AU - Huisman, Jef

AU - Free, Andrew

AU - Picioreanu, Cristian

AU - Quince, Christopher

AU - Klapper, Isaac

AU - Labarthe, Simon

AU - Smets, Barth F

AU - Wang, Harris

AU - Soyer, Orkun S

AU - Isaac Newton Institute Fellows

N1 - Acknowledgements We thank the Isaac Newton Institute of Mathematical Sciences for hosting the programme ‘Understanding microbial communities: structure, function dynamics’, which made this paper possible. This programme was partially funded by the Biotechnology and Biological Sciences Research Council and the US Army Research Office under grant number W911NF-14-1-0445. We thank all participants of the programme for inspiring discussions, and Aglika Gungova and Stela Ilieva for assistance with the figures.

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Challenges in microbial ecology: building predictive understanding of community function and dynamics

Abstract

Bibliographical note

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