Editorial policy on genome‐scale analyses (2004)

The speed with which research is conducted and the amount of information that can be generated often depend as much on the techniques employed as on the organism or system being investigated. Over the past two decades, considerable effort has been devoted to the development of new technologies and to improving existing ones. As a result, molecular microbiologists can now exploit a vast range of techniques and can perform sophisticated analyses in microorganisms that were formerly considered intractable and, even today, cannot be studied by conventional genetics. There can be no doubt that these new technologies have opened up vast areas of research in microbiology and have often revealed extraordinary and unsuspected levels of biodiversity. Major technological advances that occurred in the 17 years since Molecular Microbiology was first published include genome-scale sequencing projects, the rapid generation of gene fusions, DNA microarrays and refined hybridization techniques, functional genomic and proteomic analyses, two-hybrid analysis of protein–protein interactions and bioinformatics. The main objective of the Journal is, of course, to provide a forum for the publication of the very best of the new wave of modern microbiology. Indeed, Molecular Microbiology was among the first journals to publish genome-scale sequencing data and transcriptome analyses of complex microbial regulatory circuits. However, a new technology that has proven its worth has lost its novelty value and subsequent publications featuring it must focus more on integrating the data into a more detailed analysis of the phenomenon being studied. At the present time, a substantial proportion of the ever-increasing number of manuscripts that we receive is devoted to descriptive or comparative analyses that are based on one or other of these modern technologies. The intrinsic value of such research is rarely in doubt, nor is the substantial time and effort involved, even when part of the analysis is automated. Nevertheless, such studies, by themselves, often do not fit the Journal's remit to publish work that reveals significant new insight into molecular mechanisms underlying all aspects of microbial life. Consequently, we instigated a prescreening procedure that helps us identify those manuscripts that are unsuitable, the aim being to permit authors of such studies to resubmit their manuscripts to another, more appropriate journal as quickly as possible. For example, over 80% of the transcriptome-based manuscripts currently being submitted for publication in Molecular Microbiology are not sent out to referees because we consider them to be unsuitable. Why are so many such manuscripts considered inappropriate? While most of these papers report independent validation of the major features of the transcriptome data by alternative methods (RT-PCR, quantitative hybridization or gene fusions, for example), many do not go far enough because they do not provide insight into underlying molecular mechanisms. In theory, every regulatory circuit in every bacterium whose genome has been sequenced could be examined in this way, but should a journal like Molecular Microbiology be expected to publish all of this material, or should it be deposited in specialized databases? In these and all related cases, we believe that, as editors, we must consider the question that is being addressed. If, for example, the question is ‘What genes are affected by changing one or more factors?’ the answer will be a descriptive, data-gathering exercise and will not necessarily indicate that the changes are physiologically relevant (Birrell et al., 2002; Giaever et al., 2002). If, however, studies are performed to determine the molecular mechanisms underlying such changes, then the study is question-driven, investigative research and becomes potentially appropriate for publication in Molecular Microbiology. Thus, our editorial policy remains clear and unchanged: manuscripts reporting genome, transcriptome or proteome-wide screening approaches will only be considered suitable for publication if these components are an integral but not predominant part of a deeper, mechanistic study. We would like to stress that the decision to reject manuscripts of this type without a formal review is never taken lightly or by one editor acting alone. Instead, the editor concerned usually consults with other editors and with members of the editorial advisory board before reaching a decision in order to ensure a consistent editorial process.