Keystone taxa as drivers of microbiome structure and functioning

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Microorganisms have a pivotal role in the functioning of ecosystems. Recent studies have shown that microbial communities harbour keystone taxa, which drive community composition and function irrespective of their abundance. In this Opinion article, we propose a definition of keystone taxa in microbial ecology and summarize over 200 microbial keystone taxa that have been identified in soil, plant and marine ecosystems, as well as in the human microbiome. We explore the importance of keystone taxa and keystone guilds for microbiome structure and functioning and discuss the factors that determine their distribution and activities.

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Fig. 1: Keystone taxa in the microbiome.
Fig. 2: Keystone taxa in microbial communities and the factors influencing their functioning in an environment.
Fig. 3: Characterizing and harnessing keystone taxa.


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The authors thank the referees, whose constructive comments and insightful suggestions greatly improved the quality of the manuscript. They also thank U. Kaufmann for help with a figure and C. Stanley for proofreading the manuscript. Work in the author’s laboratory was supported by the Swiss National Science Foundation (Grant No. 31003A_166079 awarded to M.G.A.v.d.H.).

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Nature Reviews Microbiology thanks Janet Jansson and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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S.B. researched data for the article. S.B. and M.G.A.v.d.H made substantial contributions to the discussion of content and writing of the article. S.B, K.S. and M.G.A.v.d.H. reviewed and edited the manuscript before submission.

Correspondence to Samiran Banerjee or Marcel G. A. van der Heijden.

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