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.

中文翻译：

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重新审视微生物组定义：旧概念和新挑战。

过去几十年来，微生物组研究领域发展迅速，已成为科学界和公众广泛关注的话题。由于不同领域的兴趣快速增长，我们对“微生物组”一词缺乏明确的、共同商定的定义。此外，对于微生物组研究的最佳实践缺乏共识。最近，一个国际专家小组讨论了欧洲资助的微生物组支持项目框架中目前的差距。此次会议汇聚了来自不同微生物组领域的约 40 位领导者，来自世界各地的 100 多名专家参加了研讨会附带的在线调查。本文摘录了研讨会的成果以及相应的在线调查，其中包含简短的历史介绍和未来展望。我们基于 Whipps 等人提供的对该术语的紧凑、清晰和全面的描述，提出了微生物组的定义。1988 年，考虑到最新的技术发展和研究成果，修订了一系列新颖的建议。我们清楚地将微生物组和微生物群这两个术语分开，并考虑微生物组的组成、微生物组在时间和空间上的异质性和动态性、微生物网络的稳定性和恢复力、核心微生物组的定义以及功能相关的关键物种，进行了全面的讨论：以及微生物组内微生物-宿主和物种间相互作用的共同进化原理。这些广泛的定义以及建议的统一概念将有助于提高未来微生物组研究的标准化，并可能成为数据综合评估的起点，从而使知识从基础科学更快地转移到实践中。此外，微生物组标准对于解决地球健康领域人为驱动的变化相关的新挑战非常重要，其中对微生物组的理解可能发挥关键作用。