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.

TnphoA mutagenesis of Agrobacterium tumefaciens identified new extracytoplasmic protein-encoding virulence loci. Mutations in these loci conferred increased sensitivity to detergents and several antibiotics. Clones carrying these loci were isolated from an A. tumefaciens cosmid library by complementation of the detergent sensitivities of the mutants. The locus on one complementing clone was delineated by Tn5 and TnphoA mutagenesis. DNA sequence analysis of the delineated region revealed that this locus is made up of two transcriptional units, chvG and chvI, which were predicted, on the basis of amino acid sequence homology, to encode the members of a two-component sensory transduction system. The membrane-spanning sensor, a histidine protein kinase, was designated ChvG, and the response regulator, presumably a transcriptional activator, was designated ChvI. Surprisingly, ChvG was also predicted to contain a Walker type A consensus nucleotide binding site, which is unusual for sensor histidine protein kinases. Site-specific insertion mutations in either chvG or chvI abolished tumor formation ability, as well as the ability to grow on complex media. Neither the genes which are regulated nor the inducing signal is known yet for this system.