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Microbiome definition re-visited: old concepts and new challenges

Gabriele BergEnvironmental Biotechnology, Graz University of Technology, Graz, Austria. [email protected]Daria RybakovaEnvironmental Biotechnology, Graz University of Technology, Graz, AustriaDoreen FischerHelmholtz Zentrum München, Oberschleissheim, GermanyTomislav CernavaEnvironmental Biotechnology, Graz University of Technology, Graz, AustriaMarie-Christine Champomier VergèsMICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, FranceTrevor C. CharlesMetagenom Bio, 550 Parkside Drive, Unit A9, Waterloo, ON, N2L 5 V4, CanadaXiaoyulong ChenGuizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, 550025, Guizhou, ChinaLuca CocolinEuropean Food Information Council, Brussels, BelgiumKellye EversoleGema Herrero CorralMICA, INRA, 78350, Jouy-en-Josas, FranceΜαρία ΚάζουLaboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, GreeceLinda L. KinkelDepartment of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USALene LangeNélson LimaCEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, PortugalAlexander LoyDepartment of Microbial Ecology and Ecosystem Science, University of Vienna, Vienna, AustriaJames MacklinAgriculture and Agri-Food Canada, Ottawa, CanadaEmmanuelle MaguinMICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, FranceTim H. MauchlineSustainable Agriculture Sciences, Rothamsted Research, Harpenden, UKRyan McClureBiological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USABirgit MitterBioresources Unit, AIT Austrian Institute of Technology, Tulln, AustriaMatthew J. RyanCABI, Bakeham Lane, Egham, Surrey, TW20 9TY, UKInga SarandDepartment of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, EstoniaHauke SmidtLaboratory of Microbiology, Wageningen University & Research, Wageningen, the NetherlandsBettina SchelkleEuropean Food Information Council, Brussels, BelgiumHugo RoumeGeorge Seghal KiranDept of Food Science and Technology, Pondicherry University, Puducherry, IndiaJoseph SelvinDepartment of Microbiology, Pondicherry University, Puducherry, IndiaRafael Soares Correa de SouzaGenomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, BrazilL.S. van OverbeekLaboratory of Microbiology, Wageningen University & Research, Wageningen, the NetherlandsBrajesh K. SinghGlobal Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, AustraliaMichael WagnerDepartment of Microbial Ecology and Ecosystem Science, University of Vienna, Vienna, AustriaAaron M. WalshTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, IrelandAngela SessitschBioresources Unit, AIT Austrian Institute of Technology, Tulln, AustriaMichael SchloterHelmholtz Zentrum München, Oberschleissheim, Germany. [email protected]

2020en

ABI

Аннотация

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. Video Abstract.

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Идентификаторы

DOI: 10.1186/s40168-020-00875-0

Цитирования и источники

Цитирований: 6Использованных источников: 0

Показатели — AkademScholar