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Microbiome definition re-visited: old concepts and new challenges

Gabriele Berg 1 Daria Rybakova 1 Doreen Fischer 2 Tomislav Cernava 1 Marie Christine Champomier Vergès 3 Trevor Charles 4, 5 Xiaoyulong Chen 6 Luca Cocolin 7 Kellye Eversole 8 Gema Corral 9 Maria Kazou 10 Linda Kinkel 11 Lene Lange 12 Nelson Lima 13 Alexander Loy 14 James Macklin 15 Emmanuelle Maguin 3 Tim Mauchline 16 Ryan Mcclure 17 Birgit Mitter 18 Matthew Ryan 19 Inga Sarand 20 Hauke Smidt 21 Bettina Schelkle 7 Hugo Roume 22 G. Seghal Kiran 23 Joseph Selvin 23 Rafael Soares Correa de Souza 24 Leo van Overbeek 21 Brajesh Singh 25 Michael Wagner 14 Aaron Walsh 26 Angela Sessitsch 18 Michael Schloter 2
Abstract : The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role.
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Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie Christine Champomier Vergès, et al.. Microbiome definition re-visited: old concepts and new challenges. Microbiome, BioMed Central, 2020, 8, ⟨10.1186/s40168-020-00875-0⟩. ⟨hal-02939442⟩

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