Microbiome definition re-visited: old concepts and new challenges

Berg, Gabriele; Rybakova, Daria; Fischer, Doreen; Cernava, Tomislav; Vergès, Marie-Christine Champomier; Charles, Trevor; Chen, Xiaoyulong; Cocolin, Luca; Eversole, Kellye; Corral, Gema Herrero; Kazou, Maria; Kinkel, Linda; Lange, Lene; Lima, Nelson; Loy, Alexander; Macklin, James A.; Maguin, Emmanuelle; Mauchline, Tim; McClure, Ryan; Mitter, Birgit; Ryan, Matthew; Sarand, Inga; Smidt, Hauke; Schelkle, Bettina; Roume, Hugo; Kiran, G. Seghal; Selvin, Joseph; Souza, Rafael de; van Overbeek, Leo; Singh, Brajesh K.; Wagner, Michael; Walsh, Aaron; Sessitsch, Angela; Schloter, Michael

doi:10.1186/s40168-020-00875-0

Title: Microbiome definition re-visited: old concepts and new challenges

Journal Article · Tue Jun 30 00:00:00 EDT 2020 · Microbiome

DOI:https://doi.org/10.1186/s40168-020-00875-0· OSTI ID:1646830

^[1]; Rybakova, Daria ^[1]; Fischer, Doreen ^[2]; Cernava, Tomislav ^[1]; Vergès, Marie-Christine Champomier ^[3]; Charles, Trevor ^[4]; Chen, Xiaoyulong ^[5]; Cocolin, Luca ^[6]; Eversole, Kellye ^[7]; Corral, Gema Herrero ^[8]; Kazou, Maria ^[9]; Kinkel, Linda ^[10]; Lange, Lene ^[11]; Lima, Nelson ^[12]; Loy, Alexander ^[13]; Macklin, James A. ^[14]; Maguin, Emmanuelle ^[3]; Mauchline, Tim ^[15]; McClure, Ryan ^[16]; Mitter, Birgit ^[17] more »

Graz Univ. of Technology (Austria)
Helmholtz Zentrum München, Oberschleissheim (Germany)
Univ. Paris-Saclay, Jouy-en-Josas (France)
Univ. of Waterloo, ON (Canada); Metagenom Bio, Waterloo, ON (Canada)
Guizhou Univ. (China)
European Food Information Council, Brussels (Belgium)
International Alliance for Phytobiomes Research, Lee's Summit, MO (United States)
MICA, INRA, Jouy-en-Josas (France)
Agricultural Univ. of Athens (Greece)
Univ. of Minnesota, St. Paul, MN (United States)
BioEconomy, Research, & Advisory, Valby (Denmark)
Univ. of Minho, Braga (Portugal)
Univ. of Vienna (Austria)
Agriculture and Agri-Food Canada, Ottawa, ON (Canada)
Rothamsted Research, Harpenden (UK)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Austrian Inst. of Technology (AIT), Tulln (Austria)
CABI, Surrey (UK)
Tallinn Univ. of Technology (Estonia)
Wageningen University & Research, Wageningen (Netherlands)
MGP, INRA, Jouy-en-Josas (France)
Pondicherry Univ., Puducherry (India)
Universidade Estadual de Campinas (UNICAMP), Sao Paulo, Brazil
Western Sydney Univ., Penrith, NSW (Australia)
Teagasc Food Research Centre, Fermoy (Ireland)

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 uture 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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE; European Union (EU)

Grant/Contract Number:: AC05-76RL01830; 818116

OSTI ID:: 1646830

Report Number(s):: PNNL-SA-151555

Journal Information:: Microbiome, Vol. 8, Issue 1; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 703 works

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Additional file 1 of Microbiome definition re-visited: old concepts and new challenges Berg, Gabriele; Rybakova, Daria; Fischer, Doreen https://doi.org/10.6084/m9.figshare.12592671 The current record is supplemented by this text	text	January 2020
Microbiome definition re-visited: old concepts and new challenges Berg, Gabriele; Rybakova, Daria; Fischer, Doreen https://doi.org/10.6084/m9.figshare.c.5045886.v1 The current record is supplemented by this collection	collection	January 2020
Additional file 1 of Microbiome definition re-visited: old concepts and new challenges Berg, Gabriele; Rybakova, Daria; Fischer, Doreen https://doi.org/10.6084/m9.figshare.12592671.v1 The current record is supplemented by this text	text	January 2020
Microbiome definition re-visited: old concepts and new challenges Berg, Gabriele; Rybakova, Daria; Fischer, Doreen https://doi.org/10.6084/m9.figshare.c.5045886 The current record is supplemented by this collection	collection	January 2020

Title: Microbiome definition re-visited: old concepts and new challenges

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