Publishing Fundamentals

The publishing process can be broken down into different stages as shown in the diagram above. As an author, you will be responsible for the stages in green, that is conducting the research and writing and revising your paper. The stages in dark blue are a collaboration between the authors and the Society staff and you can find more details about those stages in the How to prepare your submission and Your article has been accepted, now what? How to promote your article sections of this page. The stages in light blue are the responsibility of the Society staff alongside our editors and reviewers.

When you submit your manuscript to one of our journals, it undergoes technical and ethics checks to ensure that it is compliant with our policies. Once these are complete, the manuscript is assigned to an editor whose role is to assess whether it is suitable for further consideration in the journal by ensuring it is in scope, scientifically sound and reasonably interesting.

If the editor is satisfied that your manuscript meets the journal’s criteria, they will invite peer reviewers to evaluate its scientific rigour and validity. Peer reviewers are experts in the field or the techniques you have utilised and they will use their expertise to consider if the science is robust and well communicated. Peer reviewers play a critical role in ensuring that high-quality science is published, allowing us to further advance the understanding of microbiology. More information around peer review can be found here: https://www.microbiologyresearch.org/information-for-reviewers.

Once the peer reviewers have submitted their comments, the editor will assess the manuscript once more taking into account the peer reviewers’ feedback and they will make a decision based on scientific soundness, appropriateness of method, analyses, validity of results as well as the novelty of your findings.

Once a manuscript has been accepted, it will go into production, a process by which the accepted manuscript is typeset and turned into a final html and pdf versions for publication.

Tip: Upon publication, we strongly encourage you to share your work with others and we will help to promote your paper to the wider community to increase its reach and advance the understanding of microbiology.

When preparing to submit your manuscript it is important that you ensure it is ready to be peer viewed. For example, we require that manuscripts are structured in a certain way and contain a conflict of interest statement and ethical approval. Our guidelines on how to prepare an article include a checklist to help you with this, and our Publishing Operations team will ensure all is in order by performing a number of checks before assigning your submission to an editor. This includes chekcing that the research is broadly in scope and satisfies any ethical and data requirements mandated by the journal you are submitting to.

If a manuscript does not meet the minimum criteria set out by the journal it will be returned by our office. We understand that this step may seem tedious, but these criteria are there to ensure that research can be adequately assessed by editors and reviewers. This will help speed up the process at the peer review and publication stages.

Most of the information that our editorial office requires will be captured by an online submission form, which is specific to the journal you are submitting to. We also ask you to upload a cover letter outlining your work and your reason for submitting to the journal, as well as any information you think would be important for journal staff and editors

Tip: Our Publishing Operations Editors are there to assist you from submission to publication: if you have questions or are unsure about any of these steps, feel free to email us at [email protected] and we will be happy to advise you.

Titles are the very first things editors, reviewers and readers will come across. Therefore, it is important that your title accurately summarise the key findings of your study while also being concise. Where possible, including appropriate keywords in your title will make your article more discoverable and will help your work reach the right audience and increase its dissemination. Use abbreviations sparingly and only for well-established and widely used abbreviations and acronyms.

Editors may recommend change to your title to better fit the style of the journal, so we suggest looking up some of the most recently published articles in your chosen journal to see if your title aligns with their style.

Tip: We suggest that you avoid using puns or making your title “funny”: while it could be attention-grabbing to the public, it is less likely to reach the correct audience for your work.

Requirements for abstracts vary across journals, though word counts tend to be 150-300 words. Abstracts should provide a concise, self-contained summary of your work, without abbreviations or references.

Your introductory sentences should give the wider background to your research which should be followed by a couple of sentences outlining your goal or aim in carrying out your study and a top-level summary of the methods used. Then, you should provide an overview your results and findings, briefly discussing any future research or implications for the field. Finally, remember that references should not be included in the abstract and that you should define any abbreviations you are introducing.

You should also keep in mind that journals may have specific requirement or optional features. For example, the Journal of Medical Microbiology requires structured abstracts (more information on what this means can be found here). Microbiology encourages the use of graphical abstracts, which are author-created diagrams summarising your research and which are becoming increasingly popular in scientific journals. In order to speed up the process and avoid having the manuscript sent back to you for changes, make sure you check our Information for authors page.

Tip: Use the same keywords in your initial submission form to the journal, the title and the abstract to increase discoverability of your work.

The first thing to consider is scope. Editors will reject out-of-scope papers before peer review and by making sure your work is within scope before submitting. Identifying the most suitable journal for your manuscript will help you avoid submitting to a less appropriate journal, being rejected and having to start again. If you aren’t sure, get in touch with the journal office and we will be happy to help. All journals have an ‘About’ page detailing their scope. Reading this will help you determine if your work is a good fit. Here is a top-line overview of the journals' scopes:

Tip: If you are not sure about which is the most appropriate journals for your research, don’t hesitate to ask us at [email protected].

With the rise in the number of predatory journals and dubious ethical and peer review practices in recent years, it is more important than ever to ensure your research is published in reputable and ethical journals with rigorous peer review practices.

You need to be confident your chosen journal has a suitable profile among your peers and consider, for example, if your colleagues and network publish in or read that journal. When you are thinking about the profile of a journal, it’s easy to just look for the highest impact factor you can achieve. However, a good quality community journal in your specialist area might often be a more appropriate home for your manuscript and we recommend that you consider a variety of metrics collectively instead. The Microbiology Society is a signatory of the Declaration on Research Assessment (DORA) which has been signed by hundreds of institutions, funders, societies, and publishers worldwide. This is a commitment to use a variety of metrics to measure the performance of our portfolio not just the impact factor.

Tip: You can read more about our ethics policies here: https://www.microbiologyresearch.org/ethics-policies

Publishing Open Access simply means that anyone with access to the internet, located anywhere in the world, is able to view, read and download your article free of charge.

Traditionally, journals operated on a subscription basis meaning librarians at institutions take out a subscription with a journal or publisher, and pay for access to all the content for those based at the institution. If your institution does not have a subscription, then you are unable to read the published content. This can create difficulties for researchers - for example, you would not be able to access articles relevant to your study if your institution does not have access to that specific journal.

Open Access aims to provide more equitable access to research, allowing individuals, the public, and those at institutions with less available funding to access published research. This ensures that everyone has equal access to science research, which is particularly pertinent for research that affects human health and research that is publicly funded. In this model, authors pay a fee, also known as an Article Processing Charge (APC), once their manuscript has been accepted in order to finalise their Open Access publication. The cost of this fee to publish will sometimes be incorporated into a grant proposal or covered by institutional funding.

The Microbiology Society is committed to the benefits of Open Access, but recognises that it can create barriers to publication for authors - for example, those without funding to cover the APC fee. In order to foster a truly inclusive publishing environment, the Society offers several ways to assist authors with these fees. Our Publish and Read agreements enabe correspodign authors at institutions that sign up to benefit rom uncapped Open Access publishing across our whole portfolio and unlimited access to the entire archive of Society publications. We also operates a waiver policy based on the Hinari programme. If the corresponding author of an article is based within a country in Group A or B of the HINARI list, their paper is automatically entitled to 100% APC waiver.

Tip: Make sure you check any Open Access policies your institution or funder may have and whether your funder or institution has specific Open Access requirements.

Open data encompasses a wide range of processes and principles, but at its core ensures that all relevant data for an article is freely and immediately available to anyone to reanalyse, reuse and build on. This includes generated and supporting raw data, and images, code or software; essentially, any information that has led to the conclusions presented in the research and that would allow the experimental processes described in the research to be fully reproduced by a reader.

Open data aims to increase reproducibility in the scientific literature and maintain transparency wherever possible. It ensures authors get credit for conducting the research and collecting the data first, and can generate further citations as the datasets are iterated in future work. However, there are concerns and limitations to consider. For example, sharing fully raw data at individual patient level may compromise a patient’s right to anonymity. These considerations should be balanced with the benefits of open data.

The Microbiology Society supports the aims of open data and encourages all authors submitting to any of the journals to make their supporting data fully open by depositing it with recognised and public archiving repositories, such as Figshare, Dryad, Zenodo and CodeOcean. Other methods of making supporting data available include presenting them in the main manuscript or within additional supplementary material, where appropriate. When doing so, it is important to keep in mind that when patients are involved, the data must be anonymised and not compromise patient confidentiality.

Microbial Genomics and Access Microbiology have mandatory open data policies, and authors are required to deposit and provide access to all data related to their submission. Microbial Genomics requires all sequencing data to be deposited and publicly available at submission; all other supporting data can be made privately available at point of submission for peer review, and then must be made publicly available at acceptance. Owing to the preprint stage and nature of the platform, Access Microbiology requires supporting data to be deposited and be publicly available at time of submission.

A preprint is an early version of your manuscript which you can make available online before submitting your work to a journal for publication. The key differences between preprints and published articles is that preprints do not go through editorial assessment or peer review and are simply posted in online repositories by the authors.

Sharing your research with the community as soon as possible can be valuable for your study and for the field; therefore, we encourage authors to post on preprint servers such as bioRxiv prior to submission. Once your paper has been published, make sure that the preprint is updated to indicate a Version of Record has been published by adding a link to the published paper reading '© [name of Author(s), year]. The definitive peer reviewed, edited version of this article is published in [name of Journal, volume, issue, year, DOI]”.

Access Microbiology, operates as an open research platform. When you submit an article for consideration, your manuscript will by default be posted online as a preprint in PDF format with a citable DOI, meaning you can gain credit for your work immediately and start receiving community feedback.

Tip: If you have deposited a preprint of your article in bioRxiv, you will be able to submit it directly to one of our journals from the bioRxiv server. However, if you chose to submit it direclty to us, please ensure to provide a link to the preprint in the submission form.