john r battista
Louisiana State University
Baton Rouge, United States
Specialty Chief Editor
Evolutionary and Genomic Microbiology
Advances in genome and microbiome sequencing methods have led to an unprecedented increase in microbial genome data, presenting microbiologists with the opportunity and challenge of assigning biological relevance to these sequences. Our most fundamental ideas concerning the natural history of microbial life have changed and are continuing to change because of the availability of these data. Whether from an individual organism or an environmental consortium, extracting meaning from these large and complex data sets relies on software tools that permit efficient analyses. There is not a sub-discipline within microbiology that has not benefited from integrating the traditional experimental approaches used by microbiologists with computer science and information engineering.
We envision Evolutionary and Genomic Microbiology as a vehicle for accelerating communication of basic and applied microbial research that has been informed by bioinformatic analyses to the broader community of microbiologists. Evolutionary and Genomic Microbiology publishes significant research findings on all aspects of evolutionary and genomic microbiology for Bacteria, Archaea, and unicellular Fungi. Similar information on viruses, protists, and multicellular fungi will be considered, but if deemed better suited to another journal these submissions may be transferred to a sister section within Frontiers in Microbiology or to another Frontiers journal, such as Frontiers in Virology, or Frontiers in Fungal Biology.
We seek reports that offer the potential to advance our understanding of the microbial world, its diversity, its evolution, and its ecology through application of genome sequencing and associated technologies. Evolutionary and Genomic Microbiology welcomes papers that describe:
We discourage submission of manuscripts that provide nothing more than genomic sequence and comparative predictions of gene function; there are several venues available for the direct deposit and curation of such reports and authors will be referred to these venues when appropriate.
Frontiers in Genetics is member of the Committee on Publication Ethics.
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All published articles receive a PMCID
Evolutionary and Genomic Microbiology welcomes submissions of the following article types: Correction, Editorial, Hypothesis & Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Technology and Code.
All manuscripts must be submitted directly to the section Evolutionary and Genomic Microbiology, where they are peer-reviewed by the Associate and Review Editors of the specialty section.
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That is why Frontiers provides online free and open access to all of its research publications. For more information on open access click here.
Frontiers is fully compliant with open access mandates, by publishing its articles under the Creative Commons Attribution licence (CC-BY). Funder mandates such as those by the Wellcome Trust (UK), National Institutes of Health (USA) and the Australian Research Council (Australia) are fully compatible with publishing in Frontiers. Authors retain copyright of their work and can deposit their publication in any repository. The work can be freely shared and adapted provided that appropriate credit is given and any changes specified.
Under the Frontiers Conditions for Website Use and the Frontiers General Conditions for Authors, authors of articles published in Frontiers journals retain copyright on their articles, except for any third-party images and other materials added by Frontiers, which are subject to copyright of their respective owners. Authors are therefore free to disseminate and re-publish their articles, subject to any requirements of third-party copyright owners and subject to the original publication being fully cited. The ability to copy, download, forward or otherwise distribute any materials is always subject to any copyright notices displayed. Copyright notices must be displayed prominently and may not be obliterated, deleted or hidden, totally or partially.
Each Frontiers article strives for the highest quality, thanks to genuinely collaborative interactions between authors, editors and reviewers, who include many of the world's best scientists and scholars. Frontiers is well aware of the potential impact of published research both on future research and on society and, hence, does not support superficial review, light review or no-review publishing models. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public - and shape society. Therefore, Frontiers only applies the most rigorous and unbiased reviews, established in the high standards of the Frontiers Review System. Furthermore, only the top certified research, evaluated objectively through quantitative online article level metrics, is disseminated to increasingly wider communities as it gradually climbs the tiers of the Frontiers Tiering System from specialized expert readership towards public understanding.
Frontiers has a number of procedures in place to support and ensure the quality of the research articles that are published:
Only leading experts and established members of the research community are appointed to the Frontiers Editorial Boards. Chief Editors, Associate Editors and Review Editors are all listed with their names and affiliations on the Journal pages and are encouraged to publicly list their publication credentials.
Associate Editors oversee the peer-review and take the final acceptance decision on manuscripts. Editorial decision power is distributed in Frontiers, because we believe that many experts within a community should be able to shape the direction of science for the benefit of society.
Submitting authors can choose a preferred Associate Editor to handle their manuscript, because they can judge well who would be an appropriate expert in editing their manuscript. There is no guarantee for this preference of choice, Associate Editors can decline invitations any time, and the handling Associate Editor can also be over-ridden by the Chief Editor before she/he is invited to edit the article or at any other stage.
Associate Editors are mandated to only accept to edit a manuscript if they have no conflicts of interest (as stated here and in their review invitation and assignment emails).
Should it become clear that the Associate Editor has a conflict of interest or is unable to perform the peer-review timely and adequately, a new Associate Editor can be assigned to the manuscript by the Chief Editor, who has full control to intervene in the peer-review process at any time.
The Associate Editor initially checks that the article meets basic quality standards and has no obvious objective errors.
The Associate Editor can then personally choose and invite the most appropriate reviewers to handle the peer-review of the manuscript, including Review Editors from the board or external reviewers.
The Associate Editor is aided in this by the Frontiers Collaborative Review Forum software and interface, which suggests the most relevant Review Editors based on a match between their expertise and the topic of the manuscript. Associate Editors can however choose any reviewer they deem adequate.
After a certain time frame and if no reviewers have in the meantime been assigned to the manuscript, the Frontiers platform and algorithmic safety-net steps in and invites the most appropriate Review Editors based on constantly updated and improved algorithms that match reviewer expertise with the submitted manuscript.
Review Editors and reviewers are mandated to only accept to review a manuscript if they have no conflicts of interest (as stated here and in their review invitation and assignment emails).
Frontiers algorithms are constantly fine-tuned to better match Review Editors with manuscripts, and additional checks are being coded into the platform, for example regarding conflicts of interest.
Should it become clear that a particular reviewer has a conflict of interest or is unable to perform the peer-review timely and adequately, he or she shall be replaced with an alternative reviewer by the Associate Editor or the Chief Editor, who will be alerted and has full control to intervene into the peer-review at any time.
In the Independent Review Stage the assigned reviewers perform an in-depth review of the article independently of each other to safeguard complete freedom of opinion.
The reviewers are aided by an online standardized review questionnaire – adopted to article types – with the goal to facilitate rigorous evaluation according to objective criteria and the Frontiers Review Guidelines.
The Associate Editor assesses the reviews and activates the “Interactive Review” – informing the authors of the extent of revisions that are required to address the reviewers’ comments, and starting the Interactive Discussion Forum where authors and also the reviewers get full access to all review reports.
Manuscript and review quality at this stage are enhanced by allowing authors and reviewers to discuss directly with each other in real-time until they reach consensus and a final version of the manuscript is endorsed by the reviewers.
Reviewer identity is protected at this stage to safeguard complete freedom of opinion.
Reviewers can recommend rejection at this stage if their requests to correct objective errors are not being met by the authors or if they deem the article overall of insufficient quality.
Should a dispute arise, authors or reviewers can trigger an arbitration and will alert the Associate Editor, who can assign more reviewers and/or bring the dispute to the attention of the Chief Editor. The Associate Editor can also weigh in on the discussion and is asked to mediate the process to ensure a constructive revision stage.
The decision to accept an article needs to be unanimous amongst all reviewers and the handling Associate Editor.
The names of the Associate Editor and reviewers are disclosed on published articles to encourage in depth and rigorous reviews, acknowledge work well done on the article and to bring transparency and accountability into peer-review.
Associate Editors can recommend the rejection of an article to the Chief Editor, who needs to check that the authors’ rights have been upheld during the peer-review process, and who can then ultimately reject the article if it is of insufficient quality, has objective errors or if the authors were unreasonably unwilling to address the points raised during the review.
Chief Editors can at any stage of the peer-review step in to comment on the review process, change assigned editors, assign themselves as a reviewer and even as the handling editor for the manuscript, and therefore have full authority and all the mechanisms to act independently in their online editorial office to ensure quality.
Only leading researchers acting as Associate Editors, who are not part of Frontiers staff, can make acceptance decisions based on reviews performed by external experts acting as Review Editors or reviewers. None have a financial incentive to accept articles, i.e. they are not paid for their role to act as Associate or Review Editors, and any award scheme is not linked to acceptances of manuscripts.
Chief Editors receive an honorarium if their specialty section or field reaches certain submission levels. However, this honorarium is based on the total number of submitted articles during a calendar year, and not the number of accepted articles. Therefore they also have no financial incentive to accept manuscripts.
The Frontiers platform enables post-publication commenting and discussions on papers and hence the possibility to critically evaluate articles even after the peer-review process.
Frontiers has a community retraction protocol in place to retract papers where serious concerns have been raised and validated by the community that warrant retraction, including ethical concerns, honest errors or scientific misconduct.