Microbiome definition re-visited: old concepts and new challenges

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.

The human gut microbiota is neither an organ nor a commensal

“…The aim of this work is to stimulate a discussion about the meaning of the existence of human gut microbiota in the human body and calls for caution in using terms that are becoming commonplace to describe the gut microbiota, but for which there is not yet sufficient experimental evidence supporting usage. This is not the first time that the validity of certain definitions concerning the microbiota has been questioned, for example, the terms microbiome [3] and dysbiosis [35][36], although these refer to the definitions in the literal sense of the term, while here we refer to alleged functions of the microbiota.…”

Fiber and Prebiotic Interventions in Pediatric Inflammatory Bowel Disease: What Role Does the Gut Microbiome Play?

“…The gut microbiome is an ecosystem residing within the human GI tract that comprises trillions of microorganisms such as bacteria, archaea, fungi and viruses as well as their respective genes and functions [ 71 ]. Diet, particularly fiber, is one of the key factors influencing gut microbiota composition and function [ 7 ].…”

Unveiling the Hidden Theatre of Microbes

“…The term microbiome has recently been revisited and refined [1] based on the original definition as the community of microbes (microbiota) combined with "their theatre of activities". [2] This "theatre of activities" encompasses macromolecules and mobile genetic elements as well as microbial metabolites.…”